Compositions and methods for controlling diabrotica

ABSTRACT

The present invention provides methods for controlling invertebrate pest infestations, for instance in plants, and related compositions and polynucleotides useful in such methods. More specifically, the present invention provides polynucleotides and methods of use thereof for modifying the expression of genes in an invertebrate pest, for instance through RNA interference.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.61/782,884, filed Mar. 14, 2013, herein incorporated by reference in itsentirety.

INCORPORATION OF SEQUENCE LISTINGS

The sequence listing that is contained in the file named“MONS355US.txt”, which is 699 kilobytes (as measured in MicrosoftWindows®) and was created on Mar. 11, 2014, is filed herewith byelectronic submission and is incorporated by reference herein.

FIELD OF THE INVENTION

This invention discloses methods for controlling invertebrate pestinfestations, particularly in plants, and compositions andpolynucleotides useful in such methods. More specifically, thisinvention is related to polynucleotides and methods of use thereof formodifying the expression of genes in an invertebrate pest, particularlythrough RNA interference. Particular pest species of interest includeDiabrotica species, especially those that infest crop plants.

BACKGROUND OF THE INVENTION

Commercial crops are often the targets of attack by invertebrate pestssuch as insects. Compositions for controlling insect infestations inplants have typically been in the form of chemical insecticides.However, there are several disadvantages to using chemical insecticides.For example, chemical insecticides are generally not selective, andapplications of chemical insecticides intended to control insect pestsin crop plants can exert their effects on non-target insects and otherinvertebrates as well. Chemical insecticides often persist in theenvironment and can be slow to degrade, thus potentially accumulating inthe food chain. Furthermore the use of persistent chemical insecticidescan result in the development of resistance in the target insectspecies. Thus there has been a long felt need for more environmentallyfriendly methods for controlling or eradicating insect infestation on orin plants, i. e., methods which are species-selective, environmentallyinert, non-persistent, and biodegradable, and that fit well into pestresistance management schemes.

Insecticidal compositions that include Bacillus thuringiensis (“Bt”)bacteria have been commercially available and used as environmentallysafe and acceptable insecticides for more than thirty years. Theeffectiveness of these compositions is due to insecticidal proteins thatare produced exclusively by Bt bacteria. The insecticidal Bt proteins donot persist in the environment, are highly selective as to the targetspecies affected, exert their effects only upon ingestion by a targetinsect, and have been shown to be harmless to plants and othernon-targeted organisms, including humans and other vertebrates.Transgenic plants containing one or more recombinant genes encodinginsecticidal Bt proteins are also available in the art and are resistantto insect pest infestation. One positive environmental result of the useof transgenic plants expressing Bt proteins is a decrease in the amountof chemical insecticides that are applied to control pest infestation insuch transgenic crop fields, resulting in decreased contamination ofsoil and waters by non-degraded or excess chemical insecticides. Inaddition, there has been a noticeable increase in the numbers ofbeneficial insects in fields in which Bt protein-expressing transgeniccrop plants are grown because of the decrease in the use ofnon-selective chemical insecticides.

RNA interference (RNAi, RNA-mediated gene suppression) is anotherapproach used for pest control. In invertebrates RNAi-based genesuppression was first demonstrated in nematodes (Fire et al., (1998)Nature, 391:806-811; Timmons & Fire (1998) Nature, 395:854).Subsequently, RNAi-based suppression of invertebrate genes usingrecombinant nucleic acid techniques has been reported in a number ofspecies, including agriculturally or economically important pests fromvarious insect and nematode taxa, such as: root-knot nematodes(Meloidogyne spp.), see Huang et al. (2006) Proc. Natl. Acad. Sci. USA,103:14302-14306; cotton bollworm (Helicoverpa armigera), see Mao et al.(2007) Nature Biotechnol., 25:1307-1313; Western corn rootworm(Diabrotica virgifera virgifera LeConte), see Baum et al. (2007) NatureBiotechnol., 25:1322-1326; sugar beet cyst nematode (Heteroderaschachtii), see Sindhu et al. (2008) J. Exp. Botany, 60:315-324;mosquito (Aedes aegypti), see Pridgeon et al. (2008) J. Med. Entomol.,45:414-420; fruit flies (Drosophila melanogaster), flour beetles(Tribolium castaneum), pea aphids (Acyrthosiphon pisum), and tobaccohornworms (Manduca sexta), see Whyard et al. (2009) Insect Biochem. Mol.Biol., 39:824-832; diamondback moth (Plutella xylostella), see Gong etal. (2011) Pest Manag. Sci., 67: 514-520; green peach aphid (Myzuspersicae), see Pitino et al. (2011) PLoS ONE, 6:e25709; brownplanthopper (Nilaparvata lugens), see Li et al. (2011) Pest Manag. Sci.,67:852-859; and whitefly (Bemisia tabaci), see Upadhyay et al. (2011) J.Biosci., 36:153-161.

This invention is related to methods of controlling insect pests, inparticular Diabrotica spp. which infest crop plants. This invention isfurther related to polynucleotides and recombinant DNA molecules andconstructs useful in such methods. This invention is further related toinsecticidal compositions, as well as to transgenic plants resistant toinfestation by Diabrotica spp.

This invention is also related to methods of selecting target genes thatare likely to represent essential functions, making these genespreferred targets for RNAi-mediated silencing.

SUMMARY OF THE INVENTION

This invention is related to control of Diabrotica species, especiallythose that are economically or agriculturally important pests. Thecompositions and methods of this invention include recombinantpolynucleotide molecules, such as recombinant DNA constructs for makingtransgenic plants resistant to infestation by Diabrotica species andsingle- or double-stranded DNA or RNA “triggers” that are useful, e. g.,as topically applied agents for causing RNAi-mediated suppression of atarget gene in a Diabrotica species and thus controlling or preventinginfestation by that Diabrotica species. A particular utility of thisinvention is providing maize plants, such as transgenic maize plantsexpressing a polynucleotide of this invention, or maize plants that havebeen topically treated with a polynucleotide of this invention, that areresistant to infestation by corn rootworm varieties of Diabroticaspecies. Another particular utility of this invention is apolynucleotide-containing composition that is topically applied to aDiabrotica species or to a plant to be protected from infestation by aDiabrotica species. This invention is further related to methods forselecting preferred Diabrotica target genes that are more likely to beeffective targets for RNAi-mediated control of a Diabrotica species;examples of such preferred target genes are genes that arenon-repetitive and non-redundant in a Diabrotica species genome, or thathave low nucleotide diversity, or that are evolutionarily orfunctionally constrained to have a more synonymous (K_(s)) thannonsynonymous (K_(a)) nucleotide changes.

In one aspect, this invention provides a method for controlling aDiabrotica species infestation of a plant including contacting theDiabrotica species with a polynucleotide including at least 18contiguous nucleotides with a sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof.

In another aspect, this invention provides method for controlling aDiabrotica species infestation of a plant including providing in thediet of a Diabrotica species an agent including a polynucleotide havingat least one segment of 18 or more contiguous nucleotides with asequence of about 95% to about 100% identity with a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof, whereinthe agent functions upon ingestion by the Diabrotica species to inhibita biological function within the Diabrotica species thereby controllinginfestation by the Diabrotica species.

In another aspect, this invention provides a method of causing mortalityor stunting in Diabrotica species larvae including providing in the dietof Diabrotica species larvae at least one recombinant RNA including atleast one silencing element essentially identical or essentiallycomplementary to a target gene of the Diabrotica species larvae, whereinthe target gene sequence is selected from the group consisting of SEQ IDNOs:1-450 or the complement thereof, and wherein ingestion of therecombinant RNA by the Diabrotica species larvae results in mortality orstunting in the Diabrotica species larvae.

In another aspect, this invention provides a method of providing a planthaving improved resistance to a Diabrotica species infestation includingtopically applying to the plant a composition including at least onepolynucleotide having at least one segment of 18 or more contiguousnucleotides with a sequence of about 95% to about 100% with a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof.

In another aspect, this invention provides a composition for controllinga Diabrotica species including at least one recombinant polynucleotideincluding at least 18 contiguous nucleotides that are essentiallyidentical or complementary to a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ IDNOs:1-450.

In another aspect, this invention provides a method of providing a planthaving improved resistance to a Diabrotica species infestation includingexpressing in the plant at least one polynucleotide including at least18 contiguous nucleotides that are essentially identical orcomplementary to a segment of equivalent length of a DNA having asequence selected from the group consisting of SEQ ID NOs:1-450.

In another aspect, this invention provides a recombinant DNA constructincluding a heterologous promoter operably linked to DNA including atleast one segment of 18 or more contiguous nucleotides with a sequenceof about 95% to about 100% identity with a segment of equivalent lengthof a DNA having a sequence selected from the group consisting of SEQ IDNOs:1-450 or the DNA complement thereof.

In another aspect, this invention provides a transgenic maize plant cellhaving in its genome a recombinant DNA encoding RNA that suppressesexpression of a target gene in a Diabrotica species that contacts oringests the RNA, wherein the RNA includes at least one silencing elementcomplementary to the target gene, and wherein the target gene sequenceis selected from the group consisting of SEQ ID NOs:1-450 or thecomplement thereof.

In another aspect, this invention provides an isolated recombinant RNAmolecule that causes mortality or stunting of growth in a Diabroticaspecies when ingested or contacted by the Diabrotica species, whereinthe recombinant RNA molecule includes at least 18 contiguous nucleotidesthat are essentially complementary to a segment of equivalent length ofa DNA having a sequence selected from the group consisting of SEQ IDNOs:1-450 or the DNA complement thereof.

In another aspect, this invention provides a method of providing a planthaving improved resistance to a Diabrotica species infestation includingproviding to the plant at least one polynucleotide including at least 18contiguous nucleotides that are essentially identical or complementaryto a segment of equivalent length of a DNA of a target gene selectedfrom the group consisting of the genes identified in Table 1.

In yet a further aspect, this invention provides a method forcontrolling a Diabrotica species infestation of a plant includingcontacting the Diabrotica species with a polynucleotide including atleast 18 contiguous nucleotides that are essentially identical orcomplementary to a segment of equivalent length of a DNA of a targetgene selected from the group consisting of the genes identified in Table1.

In yet a further aspect, this invention provides a method of selectingpreferred target genes for RNAi-mediated silencing from a plant genomeor from an animal genome. In various embodiments, the method provides asubset of target genes that are present in single- or low-copy-number(i. e., non-repetitive and non-redundant) in a particular genome, orthat have low nucleotide diversity, or that have a ratio of synonymous(K_(s)) to nonsynonymous (K_(a)) nucleotide changes where K_(s)>>K_(a).

In related aspects, this invention provides compositions including thepolynucleotide of this invention, such as formulations useful fortopical application to a plant or substance in need of protection from aDiabrotica species infestation, recombinant constructs and vectorsuseful for making transgenic plant cells and transgenic plants,formulations and coatings useful for treating seeds, seeds treated withor containing a polynucleotide of this invention as well as commodityproducts and foodstuffs produced from such seeds (especially commodityproducts and foodstuffs having a detectable amount of a polynucleotideof this invention). A further aspect of this invention are polyclonal ormonoclonal antibodies that bind a protein encoded by a sequence or afragment of a sequence selected from the group consisting of SEQ IDNOs:1-450; such antibodies are made by routine methods as known to oneof ordinary skill in the art.

Other aspects and specific embodiments of this invention are disclosedin the following detailed description.

DETAILED DESCRIPTION OF THE INVENTION

Unless defined otherwise, all technical and scientific terms used havethe same meaning as commonly understood by one of ordinary skill in theart to which this invention belongs. Generally, the nomenclature usedand the manufacturing or laboratory procedures described below are wellknown and commonly employed in the art. Conventional methods are usedfor these procedures, such as those provided in the art and variousgeneral references. Where a term is provided in the singular, theinventors also contemplate aspects of the invention described by theplural of that term. Where there are discrepancies in terms anddefinitions used in references that are incorporated by reference, theterms used in this application shall have the definitions given. Othertechnical terms used have their ordinary meaning in the art in whichthey are used, as exemplified by various art-specific dictionaries, forexample, “The American Heritage® Science Dictionary” (Editors of theAmerican Heritage Dictionaries, 2011, Houghton Mifflin Harcourt, Bostonand New York), the “McGraw-Hill Dictionary of Scientific and TechnicalTerms” (6^(th) edition, 2002, McGraw-Hill, New York), or the “OxfordDictionary of Biology” (6^(th) edition, 2008, Oxford University Press,Oxford and New York). The inventors do not intend to be limited to amechanism or mode of action. Reference thereto is provided forillustrative purposes only.

Unless otherwise stated, nucleic acid sequences in the text of thisspecification are given, when read from left to right, in the 5′ to 3′direction. One of skill in the art would be aware that a given DNAsequence can be understood to define a corresponding RNA sequence whichis identical to the DNA sequence except for replacement of the thymine(T) nucleotides of the DNA with uracil (U) nucleotides. Thus, providinga specific DNA sequence is understood to define the exact RNAequivalent. A given first polynucleotide sequence, whether DNA or RNA,further defines the sequence of its exact complement (which can be DNAor RNA), i. e., a second polynucleotide that hybridizes perfectly to thefirst polynucleotide by forming Watson-Crick base-pairs. By “essentiallyidentical” or “essentially complementary” to a target gene or a segmentof a target gene is meant that a polynucleotide strand (or at least onestrand of a double-stranded polynucleotide) is designed to hybridize(generally under physiological conditions such as those found in aliving plant or animal cell) to a target gene or to a segment of atarget gene or to the transcript of the target gene or the segment of atarget gene; one of skill in the art would understand that suchhybridization does not necessarily require 100% sequence identity orcomplementarity. A first nucleic acid sequence is “operably” connectedor “linked” with a second nucleic acid sequence when the first nucleicacid sequence is placed in a functional relationship with the secondnucleic acid sequence. For example, a promoter sequence is “operablylinked” to DNA if the promoter provides for transcription or expressionof the DNA. Generally, operably linked DNA sequences are contiguous.

The term “polynucleotide” commonly refers to a DNA or RNA moleculecontaining multiple nucleotides and generally refers both to“oligonucleotides” (a polynucleotide molecule of 18-25 nucleotides inlength) and longer polynucleotides of 26 or more nucleotides.Polynucleotides also include molecules containing multiple nucleotidesincluding non-canonical nucleotides or chemically modified nucleotides.Generally, polynucleotides of this invention, whether DNA or RNA orboth, and whether single- or double-stranded, include at least 18contiguous nucleotides (or, in the case of double-strandedpolynucleotides, at least 18 contiguous base-pairs) that are essentiallyidentical or complementary to a segment of equivalent size of the DNA ofa target gene or the target gene's RNA transcript. Throughout thisdisclosure, “at least 18 contiguous” means “from about 18 to about10,000, including every whole number point in between”. Thus,embodiments of this invention include compositions includingoligonucleotides having a length of 18-25 nucleotides (18-mers, 19-mers,20-mers, 21-mers, 22-mers, 23-mers, 24-mers, or 25-mers), ormedium-length polynucleotides having a length of 26 or more nucleotides(polynucleotides of 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56,57, 58, 59, 60, about 65, about 70, about 75, about 80, about 85, about90, about 95, about 100, about 110, about 120, about 130, about 140,about 150, about 160, about 170, about 180, about 190, about 200, about210, about 220, about 230, about 240, about 250, about 260, about 270,about 280, about 290, or about 300 nucleotides), or long polynucleotideshaving a length greater than about 300 nucleotides (e. g.,polynucleotides of between about 300 to about 400 nucleotides, betweenabout 400 to about 500 nucleotides, between about 500 to about 600nucleotides, between about 600 to about 700 nucleotides, between about700 to about 800 nucleotides, between about 800 to about 900nucleotides, between about 900 to about 1000 nucleotides, between about300 to about 500 nucleotides, between about 300 to about 600nucleotides, between about 300 to about 700 nucleotides, between about300 to about 800 nucleotides, between about 300 to about 900nucleotides, or about 1000 nucleotides in length, or even greater thanabout 1000 nucleotides in length, for example up to the entire length ofa target gene including coding or non-coding or both coding andnon-coding portions of the target gene). Where a polynucleotide isdouble-stranded, its length can be similarly described in terms of basepairs.

Controlling Diabrotica Infestations by Contacting with a Polynucleotide

A first aspect of this invention provides a method for controlling aDiabrotica species infestation of a plant including contacting theDiabrotica species with a polynucleotide including at least 18contiguous nucleotides with a sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof.

In various embodiments, the Diabrotica species is at least one selectedfrom the group consisting of Diabrotica balteata, Diabrotica barberi,Diabrotica beniensis, Diabrotica cristata, Diabrotica curvipustulata,Diabrotica dissimilis, Diabrotica elegantula, Diabrotica emorsitans,Diabrotica graminea, Diabrotica hispanolae, Diabrotica lemniscata,Diabrotica linsleyi, Diabrotica longicornis, Diabrotica milleri,Diabrotica nummularis, Diabrotica occlusa, Diabrotica porracea,Diabrotica scutellata, Diabrotica speciosa, Diabrotica tibialis,Diabrotica trifasciata, Diabrotica undecimpunctata, Diabroticavirgifera, and Diabrotica viridula. In specific embodiments, theDiabrotica species is at least one selected from the group consisting ofDiabrotica virgifera virgifera (Western Corn Rootworm, WCR), Diabroticaundecimpunctata howardii (Southern Corn Rootworm, SCR), Diabroticabarberi (Northern Corn Rootworm, NCR), Diabrotica virgifera zeae(Mexican Corn Rootworm, MCR), Diabrotica balteata (Brazilian CornRootworm, BZR), or Brazilian Corn Rootworm complex (BCR) consisting ofDiabrotica viridula and Diabrotica speciosa.

The plant can be any plant that is subject to infestation by aDiabrotica species. Of particular interest are embodiments wherein theplant is a row crop plant or a vegetable crop plant. Examples include aplant selected from the group consisting of maize, cucumber, squash,soybeans, and dry beans. One row crop plant of interest is maize, andembodiments include those wherein the plant is an ungerminated maizeseed, or a maize plant in a vegetative stage (from emergence totasseling stage, i. e., VE, V1, V2, V3, . . . , V(n), VT), or a maizeplant in a reproductive stage (R1, R2, R3, R4, R5, R6). One embodimentincludes maize plants in a field of maize.

The polynucleotide of this invention can be single-stranded (ss) ordouble-stranded (ds). “Double-stranded” refers to the base-pairing thatoccurs between sufficiently complementary, anti-parallel nucleic acidstrands to form a double-stranded nucleic acid structure, generallyunder physiologically relevant conditions. Embodiments of the methodinclude those wherein the polynucleotide is at least one selected fromthe group consisting of sense single-stranded DNA (ssDNA), sensesingle-stranded RNA (ssRNA), double-stranded RNA (dsRNA),double-stranded DNA (dsDNA), a double-stranded DNA/RNA hybrid,anti-sense ssDNA, or anti-sense ssRNA; a mixture of polynucleotides ofany of these types can be used.

In some embodiments, the contiguous nucleotides have a sequence of about95%, about 96%, about 97%, about 98%, about 99%, or about 100% identitywith the segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof. In some embodiments the contiguous nucleotides areexactly (100%) identical to a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ ID NOs:1-450or the DNA complement thereof. In some embodiments, the polynucleotidehas an overall sequence of about 95%, about 96%, about 97%, about 98%,about 99%, or about 100% identity with a segment of a DNA having asequence selected from the group consisting of SEQ ID NOs:1-450 or theDNA complement thereof.

Polynucleotides of use in this method include at least 18 contiguousnucleotides with a sequence of about 95% to about 100% identity with asegment of equivalent length of a DNA having a sequence selected fromthe group consisting of SEQ ID NOs:1-450 or the DNA complement thereof.The contiguous nucleotides number at least 18, e. g., between 18-24, orbetween 18-28, or between 20-30, or between 20-50, or between 20-100, orbetween 50-100, or between 100-250, or between 100-500, or between200-1000, or between 500-2000, or even greater, for example, up to theentire length of an open reading frame or up to the entire length of agene or nucleotide sequence to be suppressed. The contiguous nucleotidescan number more than 18, e. g., 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, 30, or greater than 30, e. g., about 35, about 40, about 45, about50, about 55, about 60, about 65, about 70, about 75, about 80, about85, about 90, about 95, about 100, about 110, about 120, about 130,about 140, about 150, about 160, about 170, about 180, about 190, about200, about 210, about 220, about 230, about 240, about 250, about 260,about 270, about 280, about 290, about 300, or greater than 300.

The polynucleotide of this invention is generally designed to suppressone or more genes (“target genes”). The term “gene” refers to anyportion of a nucleic acid that provides for expression of a transcriptor encodes a transcript. A “gene” thus includes, but is not limited to,a promoter region, 5′ untranslated regions, transcript encoding regionsthat can include intronic regions, and 3′ untranslated regions. Thus,the target genes can include coding or non-coding sequence or both. Inspecific embodiments, the polynucleotide is designed to suppress one ormore target genes, where each target gene has a DNA sequence selectedfrom the group consisting of SEQ ID NOs:1-450. In various embodiments,the polynucleotide is designed to suppress one or more genes, where eachgene has a sequence selected from the group consisting of SEQ IDNOs:1-450, and can be designed to suppress multiple genes from thisgroup, or to target different regions of one or more of these genes. Inan embodiment, the polynucleotide includes multiple sections or segmentseach of which includes at least 18 contiguous nucleotides with asequence of about 95% to about 100% identity with a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof. In suchcases, each section can be identical or different in size or insequence, and can be sense or anti-sense relative to the target gene.For example, in one embodiment the polynucleotide can include multiplesections in tandem or repetitive arrangements, wherein each sectionincludes at least 18 contiguous nucleotides with a sequence of about 95%to about 100% identity with a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ ID NOs:1-450or the DNA complement thereof; “spacer” nucleotides which do notcorrespond to a target gene can optionally be used in between thesections.

The total length of the polynucleotide of this invention can be greaterthan 18 contiguous nucleotides, and can include nucleotides in additionto the contiguous nucleotides having the sequence of about 95% to about100% identity with a segment of equivalent length of a DNA having asequence selected from the group consisting of SEQ ID NOs:1-450 or theDNA complement thereof. In other words, the total length of thepolynucleotide can be greater than the length of the section or segmentof the polynucleotide designed to suppress one or more target genes,where each target gene has a DNA sequence selected from the groupconsisting of SEQ ID NOs:1-450. For example, the polynucleotide can havenucleotides flanking the “active” segment of at least 18 contiguousnucleotides that suppresses the target gene, or include “spacer”nucleotides between active segments, or can have additional nucleotidesat the 5′ end, or at the 3′ end, or at both the 5′ and 3′ ends. In anembodiment, the polynucleotide can include additional nucleotides thatprovide stabilizing secondary structure.

In various embodiments the polynucleotide of this invention consists ofnaturally occurring nucleotides, such as those which occur in DNA andRNA. In certain embodiments, the polynucleotide is a combination ofribonucleotides and deoxyribonucleotides, for example, syntheticpolynucleotides consisting mainly of ribonucleotides but with one ormore terminal deoxyribonucleotides or synthetic polynucleotidesconsisting mainly of deoxyribonucleotides but with one or more terminaldideoxyribonucleotides. In certain embodiments, the polynucleotideincludes non-canonical nucleotides such as inosine, thiouridine, orpseudouridine. In certain embodiments, the polynucleotide includeschemically modified nucleotides. Examples of chemically modifiedoligonucleotides or polynucleotides are well known in the art; see, forexample, U.S. Patent Publication 2011/0171287, U.S. Patent Publication2011/0171176, U.S. Patent Publication 2011/0152353, U.S. PatentPublication 2011/0152346, and U.S. Patent Publication 2011/0160082,which are herein incorporated by reference. Illustrative examplesinclude, but are not limited to, the naturally occurring phosphodiesterbackbone of an oligonucleotide or polynucleotide which can be partiallyor completely modified with phosphorothioate, phosphorodithioate, ormethylphosphonate internucleotide linkage modifications, modifiednucleoside bases or modified sugars can be used in oligonucleotide orpolynucleotide synthesis, and oligonucleotides or polynucleotides can belabeled with a fluorescent moiety (e. g., fluorescein or rhodamine) orother label (e. g., biotin).

The polynucleotide of this invention is provided by suitable means knownto one in the art. Embodiments include those wherein the polynucleotideis chemically synthesized (e. g., by in vitro transcription, such astranscription using a T7 polymerase or other polymerase), produced byexpression in a microorganism or in cell culture (such as plant orinsect cells grown in culture), produced by expression in a plant cell,or produced by microbial fermentation.

In many embodiments the polynucleotide of this invention is provided asan isolated DNA or RNA fragment (not part of an expression construct, i.e., lacking additional elements such as a promoter or terminatorsequences). Such polynucleotides can be relatively short, such assingle- or double-stranded polynucleotides of between about 18 to about200 or about 300 nucleotides (for single-stranded polynucleotides) orbetween about 18 to about 200 or about 300 base-pairs (fordouble-stranded polynucleotides). Alternatively the polynucleotide canbe provided in more complex constructs, e. g., as part of a recombinantexpression construct, or included in a recombinant vector, for examplein a recombinant plant virus vector or in a recombinant baculovirusvector. Such recombinant expression constructs or vectors can bedesigned to include additional elements, such as expression cassettesfor expressing a gene of interest (e. g., an insecticidal protein).

In various embodiments of the method, the contacting includesapplication to a surface of the Diabrotica species of a suitablecomposition including the polynucleotide of this invention; such acomposition can be provided, e. g., as a solid, liquid (includinghomogeneous mixtures such as solutions and non-homogeneous mixtures suchas suspensions, colloids, micelles, and emulsions), powder, suspension,emulsion, spray, encapsulated or micro-encapsulation formulation, in oron microbeads or other carrier particulates, in a film or coating, or onor within a matrix. The contacting can be in the form of a seedtreatment. Suitable binders, inert carriers, surfactants, and the likecan optionally be included in the composition, as is known to oneskilled in formulation of pesticides and seed treatments. Inembodiments, the contacting includes providing the polynucleotide in acomposition that further includes one or more components selected fromthe group consisting of a carrier agent, a surfactant, anorganosilicone, a polynucleotide herbicidal molecule, anon-polynucleotide herbicidal molecule, a non-polynucleotide pesticide,a safener, and an insect growth regulator. In embodiments, thecontacting includes providing the polynucleotide in a composition thatfurther includes at least one pesticidal agent selected from the groupconsisting of a patatin, a plant lectin, a phytoecdysteroid, a Bacillusthuringiensis insecticidal protein, a Xenorhabdus insecticidal protein,a Photorhabdus insecticidal protein, a Bacillus laterosporousinsecticidal protein, and a Bacillus sphearicus insecticidal protein. Inone embodiment the contacting includes providing the polynucleotide in acomposition that can be ingested or otherwise absorbed internally by theDiabrotica species.

It is anticipated that the combination of certain polynucleotides ofthis invention (e. g., the polynucleotide triggers described in theworking Examples) with one or more non-polynucleotide pesticidal agentswill result in a synergetic improvement in prevention or control ofDiabrotica species infestations, when compared to the effect obtainedwith the polynucleotide alone or the non-polynucleotide pesticidal agentalone. In an embodiment, a composition containing one or morepolynucleotides of this invention and one or more non-polynucleotidepesticidal agent selected from the group consisting of a patatin, aplant lectin, a phytoecdysteroid, a Bacillus thuringiensis insecticidalprotein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidalprotein, a Bacillus laterosporous insecticidal protein, and a Bacillussphearicus insecticidal protein, is found to effect synergisticallyimproved prevention or control of Diabrotica species infestations.

Controlling Diabrotica Infestations by Providing a DietaryPolynucleotide

Another aspect of this invention provides a method for controlling aDiabrotica species infestation of a plant including providing in thediet of a Diabrotica species an agent including a polynucleotide havingat least one segment of 18 or more contiguous nucleotides with asequence of about 95% to about 100% identity with a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof, whereinthe agent functions upon ingestion by the Diabrotica species to inhibita biological function within the Diabrotica species thereby controllinginfestation by the Diabrotica species.

In various embodiments, the Diabrotica species is at least one selectedfrom the group consisting of Diabrotica balteata, Diabrotica barberi,Diabrotica beniensis, Diabrotica cristata, Diabrotica curvipustulata,Diabrotica dissimilis, Diabrotica elegantula, Diabrotica emorsitans,Diabrotica graminea, Diabrotica hispanolae, Diabrotica lemniscata,Diabrotica linsleyi, Diabrotica longicornis, Diabrotica milleri,Diabrotica nummularis, Diabrotica occlusa, Diabrotica porracea,Diabrotica scutellata, Diabrotica speciosa, Diabrotica tibialis,Diabrotica trifasciata, Diabrotica undecimpunctata, Diabroticavirgifera, and Diabrotica viridula. In specific embodiments, theDiabrotica species is at least one selected from the group consisting ofDiabrotica virgifera virgifera (Western Corn Rootworm, WCR), Diabroticaundecimpunctata howardii (Southern Corn Rootworm, SCR), Diabroticabarberi (Northern Corn Rootworm, NCR), Diabrotica virgifera zeae(Mexican Corn Rootworm, MCR), Diabrotica balteata (Brazilian CornRootworm, BZR), or Brazilian Corn Rootworm complex (BCR) consisting ofDiabrotica viridula and Diabrotica speciosa.

In various embodiments, the agent including a polynucleotide of thisinvention includes a microbial cell or is produced in a microorganism.For example, the agent can include or can be produced in bacteria oryeast cells. In similar embodiments the agent including a polynucleotideincludes a transgenic plant cell or is produced in a plant cell (forexample a plant cell transiently expressing the polynucleotide); suchplant cells can be cells in an plant or cells grown in tissue culture orin cell suspension.

The plant can be any plant that is subject to infestation by aDiabrotica species. Of particular interest are embodiments wherein theplant is a row crop plant or a vegetable crop plant. Examples include aplant selected from the group consisting of maize, cucumber, squash,soybeans, and dry beans. One row crop plant of interest is maize, andembodiments include those wherein the plant is an ungerminated maizeseed, or a maize plant in a vegetative stage (from emergence totasseling stage, i. e., VE, V1, V2, V3, . . . , V(n), VT), or a maizeplant in a reproductive stage (R1, R2, R3, R4, R5, R6). One embodimentincludes maize plants in a field of maize.

In various embodiments, the agent including a polynucleotide of thisinvention is provided for dietary uptake by the Diabrotica species in aform suitable for ingestion, for example, as a solid, liquid (includinghomogeneous mixtures such as solutions and non-homogeneous mixtures suchas suspensions, colloids, micelles, and emulsions), powder, suspension,emulsion, spray, encapsulated or micro-encapsulation formulation, in oron microbeads or other carrier particulates, in a film or coating, or onor within a matrix. The agent including a polynucleotide can be providedfor dietary uptake by the Diabrotica species by applying the agent to aplant subject to infestation by the Diabrotica species, for example byspraying, dusting, or coating the plant, or by application of a soildrench, or by providing in an artificial diet. The agent including apolynucleotide can be provided for dietary uptake by the Diabroticaspecies in an artificial diet formulated to meet the particularnutritional requirements for maintaining the Diabrotica species, whereinthe artificial diet is supplemented with some amount of thepolynucleotide obtained from a separate source such as chemicalsynthesis or purified from a microbial fermentation; this embodiment canbe useful, e. g., for determining the timing and amounts of effectivepolynucleotide treatment regimes. In some embodiments the agentincluding a polynucleotide is provided for dietary uptake by theDiabrotica species in the form of a plant cell or in plant cellcomponents, or in a microorganism (such as a bacterium or a yeast) or amicrobial fermentation product, or in a synthetic diet. In oneembodiment the agent including a polynucleotide is provided in the formof bait that is ingested by the Diabrotica species. The agent includinga polynucleotide can be provided for dietary uptake by the Diabroticaspecies in the form of a seed treatment. Suitable binders, inertcarriers, surfactants, and the like can be included in the agent, as isknown to one skilled in formulation of pesticides and seed treatments.In embodiments, the agent including a polynucleotide further includesone or more components selected from the group consisting of a carrieragent, a surfactant, an organosilicone, a polynucleotide herbicidalmolecule, a non-polynucleotide herbicidal molecule, a non-polynucleotidepesticide, a safener, and an insect growth regulator. In embodiments,the agent including a polynucleotide further includes at least onepesticidal agent selected from the group consisting of a patatin, aplant lectin, a phytoecdysteroid, a phytoecdysteroid, a Bacillusthuringiensis insecticidal protein, a Xenorhabdus insecticidal protein,a Photorhabdus insecticidal protein, a Bacillus laterosporousinsecticidal protein, and a Bacillus sphearicus insecticidal protein.

It is anticipated that the combination of certain polynucleotides of usein agents of this invention (e. g., the polynucleotide triggersdescribed in the working Examples) with one or more non-polynucleotidepesticidal agents will result in a synergetic improvement in preventionor control of Diabrotica species infestations, when compared to theeffect obtained with the polynucleotide alone or the non-polynucleotidepesticidal agent alone. In an embodiment, a composition containing oneor more polynucleotides of this invention and one or morenon-polynucleotide pesticidal agent selected from the group consistingof a patatin, a plant lectin, a phytoecdysteroid, a Bacillusthuringiensis insecticidal protein, a Xenorhabdus insecticidal protein,a Photorhabdus insecticidal protein, a Bacillus laterosporousinsecticidal protein, and a Bacillus sphearicus insecticidal protein, isfound to effect synergistically improved prevention or control ofDiabrotica species infestations when provided to the Diabrotica speciesin a diet.

The polynucleotide of use in agents of this invention can besingle-stranded (ss) or double-stranded (ds). “Double-stranded” refersto the base-pairing that occurs between sufficiently complementary,anti-parallel nucleic acid strands to form a double-stranded nucleicacid structure, generally under physiologically relevant conditions.Embodiments of the method include those wherein the polynucleotide is atleast one selected from the group consisting of sense single-strandedDNA (ssDNA), sense single-stranded RNA (ssRNA), double-stranded RNA(dsRNA), double-stranded DNA (dsDNA), a double-stranded DNA/RNA hybrid,anti-sense ssDNA, or anti-sense ssRNA; a mixture of polynucleotides ofany of these types can be used.

In some embodiments, the contiguous nucleotides have a sequence of about95%, about 96%, about 97%, about 98%, about 99%, or about 100% identitywith the segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof. In some embodiments the contiguous nucleotides areexactly (100%) identical to a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ ID NOs:1-450or the DNA complement thereof. In some embodiments, the polynucleotidehas an overall sequence of about 95%, about 96%, about 97%, about 98%,about 99%, or about 100% identity with a segment of a DNA having asequence selected from the group consisting of SEQ ID NOs:1-450 or theDNA complement thereof.

Polynucleotides of use in agents of this invention include at least 18contiguous nucleotides with a sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof. The contiguous nucleotides number at least 18, e.g., between 18-24, or between 18-28, or between 20-30, or between 20-50,or between 20-100, or between 50-100, or between 100-250, or between100-500, or between 200-1000, or between 500-2000, or even greater, forexample, up to the entire length of an open reading frame or up to theentire length of a gene or nucleotide sequence to be suppressed. Thecontiguous nucleotides can number more than 18, e. g., 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, or greater than 30, e. g., about 35,about 40, about 45, about 50, about 55, about 60, about 65, about 70,about 75, about 80, about 85, about 90, about 95, about 100, about 110,about 120, about 130, about 140, about 150, about 160, about 170, about180, about 190, about 200, about 210, about 220, about 230, about 240,about 250, about 260, about 270, about 280, about 290, about 300, orgreater than 300.

The polynucleotide of use in agents of this invention is generallydesigned to suppress one or more genes (“target genes”). The term “gene”refers to any portion of a nucleic acid that provides for expression ofa transcript or encodes a transcript. A “gene” thus includes, but is notlimited to, a promoter region, 5′ untranslated regions, transcriptencoding regions that can include intronic regions, and 3′ untranslatedregions. Thus, the target genes can include coding or non-codingsequence or both. In specific embodiments, the polynucleotide isdesigned to suppress one or more target genes, where each target genehas a DNA sequence selected from the group consisting of SEQ IDNOs:1-450. In various embodiments, the polynucleotide is designed tosuppress one or more genes, where each gene has a sequence selected fromthe group consisting of SEQ ID NOs:1-450, and can be designed tosuppress multiple genes from this group, or to target different regionsof one or more of these genes. In an embodiment, the polynucleotideincludes multiple sections or segments each of which includes at least18 contiguous nucleotides with a sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof. In such cases, each section can be identical ordifferent in size or in sequence, and can be sense or anti-senserelative to the target gene. For example, in one embodiment thepolynucleotide can include multiple sections in tandem or repetitivearrangements, wherein each section includes at least 18 contiguousnucleotides with a sequence of about 95% to about 100% identity with asegment of equivalent length of a DNA having a sequence selected fromthe group consisting of SEQ ID NOs:1-450 or the DNA complement thereof;“spacer” nucleotides which do not correspond to a target gene canoptionally be used in between the sections.

The total length of the polynucleotide of use in agents of thisinvention can be greater than 18 contiguous nucleotides, and can includenucleotides in addition to the contiguous nucleotides having thesequence of about 95% to about 100% identity with a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof. In otherwords, the total length of the polynucleotide can be greater than thelength of the section or segment of the polynucleotide designed tosuppress one or more target genes, where each target gene has a DNAsequence selected from the group consisting of SEQ ID NOs:1-450. Forexample, the polynucleotide can have nucleotides flanking the “active”segment of at least 18 contiguous nucleotides that suppresses the targetgene, or include “spacer” nucleotides between active segments, or canhave additional nucleotides at the 5′ end, or at the 3′ end, or at boththe 5′ and 3′ ends. In an embodiment, the polynucleotide can includeadditional nucleotides that provide stabilizing secondary structure.

In various embodiments the polynucleotide of use in agents of thisinvention consists of naturally occurring nucleotides, such as thosewhich occur in DNA and RNA. In certain embodiments, the polynucleotideis a combination of ribonucleotides and deoxyribonucleotides, forexample, synthetic polynucleotides consisting mainly of ribonucleotidesbut with one or more terminal deoxyribonucleotides or syntheticpolynucleotides consisting mainly of deoxyribonucleotides but with oneor more terminal dideoxyribonucleotides. In certain embodiments, thepolynucleotide includes non-canonical nucleotides such as inosine,thiouridine, or pseudouridine. In certain embodiments, thepolynucleotide includes chemically modified nucleotides. Examples ofchemically modified oligonucleotides or polynucleotides are well knownin the art; see, for example, U.S. Patent Publication 2011/0171287, U.S.Patent Publication 2011/0171176, U.S. Patent Publication 2011/0152353,U.S. Patent Publication 2011/0152346, and U.S. Patent Publication2011/0160082, which are herein incorporated by reference. Illustrativeexamples include, but are not limited to, the naturally occurringphosphodiester backbone of an oligonucleotide or polynucleotide whichcan be partially or completely modified with phosphorothioate,phosphorodithioate, or methylphosphonate internucleotide linkagemodifications, modified nucleoside bases or modified sugars can be usedin oligonucleotide or polynucleotide synthesis, and oligonucleotides orpolynucleotides can be labeled with a fluorescent moiety (e. g.,fluorescein or rhodamine) or other label (e. g., biotin).

The polynucleotide of use in agents of this invention is provided bysuitable means known to one in the art. Embodiments include thosewherein the polynucleotide is chemically synthesized (e. g., by in vitrotranscription, such as transcription using a T7 polymerase or otherpolymerase), produced by expression in a microorganism or in cellculture (such as plant or insect cells grown in culture), produced byexpression in a plant cell, or produced by microbial fermentation.

In many embodiments the polynucleotide of use in agents of thisinvention is provided as an isolated DNA or RNA fragment (not part of anexpression construct, i. e., lacking additional elements such as apromoter or terminator sequences). Such polynucleotides can berelatively short, such as single- or double-stranded polynucleotides ofbetween about 18 to about 200 or about 300 nucleotides (forsingle-stranded polynucleotides) or between about 18 to about 200 orabout 300 base-pairs (for double-stranded polynucleotides).Alternatively the polynucleotide can be provided in more complexconstructs, e. g., as part of a recombinant expression construct, orincluded in a recombinant vector, for example in a recombinant plantvirus vector or in a recombinant baculovirus vector. Such recombinantexpression constructs or vectors can be designed to include additionalelements, such as expression cassettes for expressing a gene of interest(e. g., an insecticidal protein).

Controlling Diabrotica Infestations by Providing a Dietary RecombinantRNA

Another aspect of this invention provides a method of causing mortalityor stunting in Diabrotica species larvae including providing in the dietof Diabrotica species larvae at least one recombinant RNA including atleast one silencing element, wherein the at least one silencing elementis essentially identical or essentially complementary to a target geneof the Diabrotica species larvae, wherein the target gene sequence isselected from the group consisting of SEQ ID NOs:1-450 or the complementthereof, and wherein ingestion of the recombinant RNA by the Diabroticaspecies larvae results in mortality or stunting in the Diabroticaspecies larvae. A related aspect of this invention is the recombinantRNA including at least one silencing element, wherein the at least onesilencing element is essentially identical or essentially complementaryto a target gene of the Diabrotica species larvae, wherein the targetgene sequence is selected from the group consisting of SEQ ID NOs:1-450or the complement thereof.

In various embodiments, the Diabrotica species is at least one selectedfrom the group consisting of Diabrotica balteata, Diabrotica barberi,Diabrotica beniensis, Diabrotica cristata, Diabrotica curvipustulata,Diabrotica dissimilis, Diabrotica elegantula, Diabrotica emorsitans,Diabrotica graminea, Diabrotica hispanolae, Diabrotica lemniscata,Diabrotica linsleyi, Diabrotica longicornis, Diabrotica milleri,Diabrotica nummularis, Diabrotica occlusa, Diabrotica porracea,Diabrotica scutellata, Diabrotica speciosa, Diabrotica tibialis,Diabrotica trifasciata, Diabrotica undecimpunctata, Diabroticavirgifera, and Diabrotica viridula. In specific embodiments, theDiabrotica species is at least one selected from the group consisting ofDiabrotica virgifera virgifera (Western Corn Rootworm, WCR), Diabroticaundecimpunctata howardii (Southern Corn Rootworm, SCR), Diabroticabarberi (Northern Corn Rootworm, NCR), Diabrotica virgifera zeae(Mexican Corn Rootworm, MCR), Diabrotica balteata (Brazilian CornRootworm, BZR), or Brazilian Corn Rootworm complex (BCR) consisting ofDiabrotica viridula and Diabrotica speciosa.

In various embodiments, the diet providing the recombinant RNA includesa microbial cell or is produced in a microorganism. For example, thediet providing the recombinant RNA can include or can be produced inbacteria or yeast cells. In similar embodiments the diet providing therecombinant RNA includes a transgenic plant cell or is produced in aplant cell (for example a plant cell transiently expressing thepolynucleotide); such plant cells can be cells in an plant or cellsgrown in tissue culture or in cell suspension.

In one embodiment the diet providing the recombinant RNA is any plantthat is subject to infestation by a Diabrotica species, wherein therecombinant RNA is contained in or on the plant. Such plants can bestably transgenic plants that express the recombinant RNA, ornon-transgenic plants that transiently express the recombinant RNA.Stably transgenic plants generally contain integrated into their genomea recombinant construct that encodes the recombinant RNA. Of particularinterest are embodiments wherein the plant is a row crop plant or avegetable crop plant. Examples include a plant selected from the groupconsisting of maize, cucumber, squash, soybeans, and dry beans. One rowcrop plant of interest is maize, and embodiments include those whereinthe plant is an ungerminated maize seed, or a maize plant in avegetative stage (from emergence to tasseling stage, i. e., VE, V1, V2,V3, . . . , V(n), VT), or a maize plant in a reproductive stage (R1, R2,R3, R4, R5, R6). One embodiment includes maize plants in a field ofmaize.

In various embodiments, the diet providing the recombinant RNA isprovided in a form suitable for ingestion by the Diabrotica species, forexample, as a solid, liquid (including homogeneous mixtures such assolutions and non-homogeneous mixtures such as suspensions, colloids,micelles, and emulsions), powder, suspension, emulsion, spray,encapsulated or micro-encapsulation formulation, in or on microbeads orother carrier particulates, in a film or coating, or on or within amatrix. The diet providing the recombinant RNA can be provided byapplying the diet to a plant subject to infestation by the Diabroticaspecies, for example by spraying, dusting, or coating the plant, or byapplication of a soil drench, or by providing in an artificial diet. Inone embodiment the diet providing the recombinant RNA is provided in theform of bait that is ingested by the Diabrotica species. The dietproviding the recombinant RNA can be an artificial diet formulated tomeet the particular nutritional requirements for maintaining theDiabrotica species, wherein the artificial diet is supplemented withsome amount of the recombinant RNA obtained from a separate source suchas chemical synthesis or purified from a microbial fermentation; thisembodiment can be useful, e. g., for determining the timing and amountsof effective polynucleotide treatment regimes. In some embodiments thediet providing the recombinant RNA is provided in the form of a plantcell or in plant cell components, or in a microorganism (such as abacterium or a yeast) or a microbial fermentation product, or in asynthetic diet. In one embodiment the diet providing the recombinant RNAis provided in the form of bait that is ingested by the Diabroticaspecies. The diet providing the recombinant RNA can be provided in theform of a seed treatment. Suitable binders, inert carriers, surfactants,and the like can be included in the diet, as is known to one skilled informulation of pesticides and seed treatments. In embodiments, the dietproviding the recombinant RNA further includes one or more componentsselected from the group consisting of a carrier agent, a surfactant, anorganosilicone, a polynucleotide herbicidal molecule, anon-polynucleotide herbicidal molecule, a non-polynucleotide pesticide,a safener, and an insect growth regulator. In embodiments, the dietproviding the recombinant RNA further includes at least one pesticidalagent selected from the group consisting of a patatin, a plant lectin, aphytoecdysteroid, a Bacillus thuringiensis insecticidal protein, aXenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, aBacillus laterosporous insecticidal protein, and a Bacillus sphearicusinsecticidal protein.

It is anticipated that the combination of certain recombinant RNAs ofthis invention (e. g., the dsRNA triggers described in the workingExamples) with one or more non-polynucleotide pesticidal agents willresult in a synergetic improvement in prevention or control ofDiabrotica species infestations, when compared to the effect obtainedwith the recombinant RNA alone or the non-polynucleotide pesticidalagent alone. In an embodiment, a composition containing one or morerecombinant RNAs of this invention and one or more non-polynucleotidepesticidal agent selected from the group consisting of a patatin, aplant lectin, a phytoecdysteroid, a Bacillus thuringiensis insecticidalprotein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidalprotein, a Bacillus laterosporous insecticidal protein, and a Bacillussphearicus insecticidal protein, is found to effect synergisticallyimproved prevention or control of Diabrotica species infestations.

The recombinant RNA of this invention can be single-stranded (ss) ordouble-stranded (ds). “Double-stranded” refers to the base-pairing thatoccurs between sufficiently complementary, anti-parallel nucleic acidstrands to form a double-stranded nucleic acid structure, generallyunder physiologically relevant conditions. Embodiments of the methodinclude those wherein the recombinant RNA is at least one selected fromthe group consisting of sense single-stranded RNA (ssRNA), anti-sensesingle-stranded (ssRNA), or double-stranded RNA (dsRNA); a mixture ofrecombinant RNAs of any of these types can be used. In one embodiment adouble-stranded DNA/RNA hybrid can be used.

The at least one recombinant RNA of this invention includes at least onesilencing element, wherein the silencing element is essentiallyidentical (as the RNA equivalent) or essentially complementary to atarget gene of the Diabrotica species larvae, wherein the target genesequence is selected from the group consisting of SEQ ID NOs:1-450 orthe complement thereof. In some embodiments, the silencing element has asequence of about 95%, about 96%, about 97%, about 98%, about 99%, orabout 100% identity with a segment of equivalent length of a DNA havinga sequence selected from the group consisting of SEQ ID NOs:1-450 or theDNA complement thereof. In some embodiments the silencing element isexactly (100%) identical (as the RNA equivalent) to a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof. In someembodiments, the silencing element has an overall sequence of about 95%,about 96%, about 97%, about 98%, about 99%, or about 100% identity withthe segment of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof.

In some embodiments, the silencing element includes at least 18contiguous nucleotides with a sequence of about 95% to about 100% with asegment of equivalent length of the target gene. In some embodiments thesilencing element includes at least 18 contiguous nucleotides with asequence of about 95% to about 100% identity with a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof. In someembodiments the silencing element includes at least 18 contiguousnucleotides, e. g., between 18-24, or between 18-28, or between 20-30,or between 20-50, or between 20-100, or between 50-100, or between100-250, or between 100-500, or between 200-1000 contiguous nucleotides.In some embodiments the silencing element includes more than 18contiguous nucleotides, e. g., 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, 30, or greater than 30, e. g., about 35, about 40, about 45, about50, about 55, about 60, about 65, about 70, about 75, about 80, about85, about 90, about 95, about 100, about 110, about 120, about 130,about 140, about 150, about 160, about 170, about 180, about 190, about200, about 210, about 220, about 230, about 240, about 250, about 260,about 270, about 280, about 290, about 300, or greater than 300contiguous nucleotides.

The recombinant RNA of this invention is generally designed to suppressone or more genes (“target genes”). Such target genes can include codingor non-coding sequence or both. In specific embodiments, the recombinantRNA is designed to suppress one or more target genes, where each targetgene has a DNA sequence selected from the group consisting of SEQ IDNOs:1-450. In various embodiments, the recombinant RNA is designed tosuppress one or more genes, where each gene has a sequence selected fromthe group consisting of SEQ ID NOs:1-450, and can be designed tosuppress multiple genes from this group, or to target different regionsof one or more of these genes. In an embodiment, the recombinant RNAincludes multiple silencing elements each of which includes at least 18contiguous nucleotides with a sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof. In such cases, each silencing element can beidentical or different in size or in sequence, and can be sense oranti-sense relative to the target gene. For example, in one embodimentthe polynucleotide can include multiple silencing elements in tandem orrepetitive arrangements, wherein each silencing element includes atleast 18 contiguous nucleotides with a sequence of about 95% to about100% identity with a segment of equivalent length of a DNA having asequence selected from the group consisting of SEQ ID NOs:1-450 or theDNA complement thereof; “spacer” nucleotides which do not correspond toa target gene can optionally be used in between the silencing elements.

The total length of the recombinant RNA of this invention can be greaterthan 18 contiguous nucleotides, and can include nucleotides in additionto the silencing element having the sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof. In other words, the total length of the recombinantRNA can be greater than the length of the silencing element designed tosuppress one or more target genes, where each target gene has a DNAsequence selected from the group consisting of SEQ ID NOs:1-450. Forexample, the recombinant RNA can have nucleotides flanking the “active”silencing element of at least 18 contiguous nucleotides that suppressesthe target gene, or include “spacer” nucleotides between activesilencing element, or can have additional nucleotides at the 5′ end, orat the 3′ end, or at both the 5′ and 3′ ends. In an embodiment, therecombinant RNA can include additional nucleotides that providestabilizing secondary structure.

In various embodiments the recombinant RNA of this invention consists ofnaturally occurring ribonucleotides. In other embodiments therecombinant RNA is chemically modified, or includes chemically modifiednucleotides. The recombinant RNA is provided by suitable means known toone in the art. Embodiments include those wherein the recombinant RNA ischemically synthesized (e. g., by in vitro transcription, such astranscription using a T7 polymerase or other polymerase), produced byexpression in a microorganism or in cell culture (such as plant orinsect cells grown in culture), produced by expression in a plant cell,or produced by microbial fermentation.

In many embodiments the recombinant RNA of this invention is provided asan isolated RNA fragment. Such RNAs can be relatively short, such assingle- or double-stranded RNAs of between about 18 to about 200 orabout 300 nucleotides (for single-stranded RNAs) or between about 18 toabout 200 or about 300 base-pairs (for double-stranded RNAs).Alternatively the recombinant RNA can be provided in more complexconstructs, e. g., including additional RNA encoding an aptamer orribozyme or an insecticidal protein.

Methods of Providing Plants Having Improved Resistance to DiabroticaInfestations, and the Plants and Seeds Thus Provided

Another aspect of this invention provides a method of providing a planthaving improved resistance to a Diabrotica species infestation includingtopically applying to the plant a composition including at least onepolynucleotide having at least one segment of 18 or more contiguousnucleotides with a sequence of about 95% to about 100% identity with asegment of equivalent length of a DNA having a sequence selected fromthe group consisting of SEQ ID NOs:1-450 or the DNA complement thereof,whereby the plant treated with the polynucleotide composition exhibitsimproved resistance to a Diabrotica species infestation, relative to anuntreated plant. In an embodiment the at least one polynucleotideincludes at least 18 contiguous nucleotides that are essentiallyidentical or complementary to a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ IDNOs:1-450.

The plant can be any plant that is subject to infestation by aDiabrotica species. Of particular interest are embodiments wherein theplant is a row crop plant or a vegetable crop plant. Examples include aplant selected from the group consisting of maize, cucumber, squash,soybeans, and dry beans. One row crop plant of interest is maize, andembodiments include those wherein the plant is an ungerminated maizeseed, or a maize plant in a vegetative stage (from emergence totasseling stage, i. e., VE, V1, V2, V3, . . . , V(n), VT), or a maizeplant in a reproductive stage (R1, R2, R3, R4, R5, R6). One embodimentincludes maize plants in a field of maize.

In various embodiments, the Diabrotica species is at least one selectedfrom the group consisting of Diabrotica balteata, Diabrotica barberi,Diabrotica beniensis, Diabrotica cristata, Diabrotica curvipustulata,Diabrotica dissimilis, Diabrotica elegantula, Diabrotica emorsitans,Diabrotica graminea, Diabrotica hispanolae, Diabrotica lemniscata,Diabrotica linsleyi, Diabrotica longicornis, Diabrotica milleri,Diabrotica nummularis, Diabrotica occlusa, Diabrotica porracea,Diabrotica scutellata, Diabrotica speciosa, Diabrotica tibialis,Diabrotica trifasciata, Diabrotica undecimpunctata, Diabroticavirgifera, and Diabrotica viridula. In specific embodiments, theDiabrotica species is at least one selected from the group consisting ofDiabrotica virgifera virgifera (Western Corn Rootworm, WCR), Diabroticaundecimpunctata howardii (Southern Corn Rootworm, SCR), Diabroticabarberi (Northern Corn Rootworm, NCR), Diabrotica virgifera zeae(Mexican Corn Rootworm, MCR), Diabrotica balteata (Brazilian CornRootworm, BZR), or Brazilian Corn Rootworm complex (BCR) consisting ofDiabrotica viridula and Diabrotica speciosa.

By “topical application” is meant application to the surface or exteriorof an object, such as the surface or exterior of a plant, such asapplication to the surfaces of a plant part such as a leaf, stem,flower, fruit, shoot, root, seed, tuber, flowers, anthers, or pollen, orapplication to an entire plant, or to the above-ground or below-groundportions of a plant. Topical application can be carried out onnon-living surfaces, such as application to soil, or to a surface ormatrix by which a Diabrotica insect can come in contact with thepolynucleotide. In various embodiments of the method, the compositionincluding at least one polynucleotide is topically applied to the plantin a suitable form, e. g., as a solid, liquid (including homogeneousmixtures such as solutions and non-homogeneous mixtures such assuspensions, colloids, micelles, and emulsions), powder, suspension,emulsion, spray, encapsulated or micro-encapsulation formulation, in oron microbeads or other carrier particulates, in a film or coating, or onor within a matrix. Topical application of the polynucleotide-containingcomposition to the plant can be in the form of a seed treatment.Suitable binders, inert carriers, surfactants, and the like canoptionally be included in the composition, as is known to one skilled informulation of pesticides and seed treatments. In one embodiment thepolynucleotide-containing composition can be ingested or otherwiseabsorbed internally by the Diabrotica species. For example, thepolynucleotide-containing composition can be in the form of bait. Inembodiments, the polynucleotide-containing composition further includesone or more components selected from the group consisting of a carrieragent, a surfactant, an organosilicone, a polynucleotide herbicidalmolecule, a non-polynucleotide herbicidal molecule, a non-polynucleotidepesticide, a safener, and an insect growth regulator. In one embodimentthe composition further includes a nonionic organosilicone surfactantsuch as Silwet, e. g., Silwet® L-77 surfactant having CAS Number27306-78-1 and EPA Number: CAL.REG.NO. 5905-50073-AA, currentlyavailable from Momentive Performance Materials, Albany, N.Y. Inembodiments, the topically applied composition further includes at leastone pesticidal agent selected from the group consisting of a patatin, aplant lectin, a phytoecdysteroid, a Bacillus thuringiensis insecticidalprotein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidalprotein, a Bacillus laterosporous insecticidal protein, and a Bacillussphearicus insecticidal protein. Alternatively such additionalcomponents or pesticidal agents can be provided separately, e. g., byseparate topical application or by transgenic expression in the plant.Alternatively the plant is topically treated with thepolynucleotide-containing composition as well as with a separate(preceding, following, or concurrent) application of a substance thatimproves the efficacy of the polynucleotide-containing composition. Forexample, a plant can be sprayed with a first topical application of asolution containing a nonionic organosilicone surfactant such as Silwet,e. g., Silwet® L-77, followed by a second topical application of thepolynucleotide-containing composition, or vice-versa.

It is anticipated that the combination of certain polynucleotides usefulin compositions of this invention (e. g., the polynucleotide triggersdescribed in the working Examples) with one or more non-polynucleotidepesticidal agents will result in a synergetic improvement in preventionor control of Diabrotica species infestations, when compared to theeffect obtained with the polynucleotide alone or the non-polynucleotidepesticidal agent alone. In an embodiment, a transgenic plant expressingone or more polynucleotides of this invention and one or more genesencoding a non-polynucleotide pesticidal agent selected from the groupconsisting of a patatin, a plant lectin, a phytoecdysteroid, a Bacillusthuringiensis insecticidal protein, a Xenorhabdus insecticidal protein,a Photorhabdus insecticidal protein, a Bacillus laterosporousinsecticidal protein, and a Bacillus sphearicus insecticidal protein, isfound to exhibit synergistically improved resistance to Diabroticaspecies infestations.

In some embodiments of the method, the composition including at leastone polynucleotide is topically applied to above-ground parts of theplant, e. g., sprayed or dusted onto leaves, stems, and flowering partsof the plant. In other embodiments, the composition including at leastone polynucleotide is topically applied to below-ground parts of theplant, such as to the roots, e. g., by means of a soil drench. In otherembodiments, the composition including at least one polynucleotide istopically applied to a seed that is grown into the plant.

The polynucleotide useful in compositions of this invention can besingle-stranded (ss) or double-stranded (ds). “Double-stranded” refersto the base-pairing that occurs between sufficiently complementary,anti-parallel nucleic acid strands to form a double-stranded nucleicacid structure, generally under physiologically relevant conditions.Embodiments of the method include those wherein the polynucleotide is atleast one selected from the group consisting of sense single-strandedDNA (ssDNA), sense single-stranded RNA (ssRNA), double-stranded RNA(dsRNA), double-stranded DNA (dsDNA), a double-stranded DNA/RNA hybrid,anti-sense ssDNA, or anti-sense ssRNA; a mixture of polynucleotides ofany of these types can be used.

In various embodiments the polynucleotide useful in compositions of thisinvention consists of naturally occurring nucleotides, such as thosewhich occur in DNA and RNA. In certain embodiments, the polynucleotideis a combination of ribonucleotides and deoxyribonucleotides, forexample, synthetic polynucleotides consisting mainly of ribonucleotidesbut with one or more terminal deoxyribonucleotides or syntheticpolynucleotides consisting mainly of deoxyribonucleotides but with oneor more terminal dideoxyribonucleotides. In certain embodiments, thepolynucleotide includes non-canonical nucleotides such as inosine,thiouridine, or pseudouridine. In certain embodiments, thepolynucleotide includes chemically modified nucleotides. Examples ofchemically modified oligonucleotides or polynucleotides are well knownin the art; see, for example, U.S. Patent Publication 2011/0171287, U.S.Patent Publication 2011/0171176, U.S. Patent Publication 2011/0152353,U.S. Patent Publication 2011/0152346, and U.S. Patent Publication2011/0160082, which are herein incorporated by reference. Illustrativeexamples include, but are not limited to, the naturally occurringphosphodiester backbone of an oligonucleotide or polynucleotide whichcan be partially or completely modified with phosphorothioate,phosphorodithioate, or methylphosphonate internucleotide linkagemodifications, modified nucleoside bases or modified sugars can be usedin oligonucleotide or polynucleotide synthesis, and oligonucleotides orpolynucleotides can be labeled with a fluorescent moiety (e. g.,fluorescein or rhodamine) or other label (e. g., biotin).

The polynucleotide useful in compositions of this invention is providedby suitable means known to one in the art. Embodiments include thosewherein the polynucleotide is chemically synthesized (e. g., by in vitrotranscription, such as transcription using a T7 polymerase or otherpolymerase), produced by expression in a microorganism or in cellculture (such as plant or insect cells grown in culture), produced byexpression in a plant cell, or produced by microbial fermentation.

In many embodiments the polynucleotide useful in compositions of thisinvention is provided as an isolated DNA or RNA fragment (not part of anexpression construct, i. e., lacking additional elements such as apromoter or terminator sequences). Such polynucleotides can berelatively short, such as single- or double-stranded polynucleotides ofbetween about 18 to about 200 or about 300 nucleotides (forsingle-stranded polynucleotides) or between about 18 to about 200 orabout 300 base-pairs (for double-stranded polynucleotides).Alternatively the polynucleotide can be provided in more complexconstructs, e. g., as part of a recombinant expression construct, orincluded in a recombinant vector, for example in a recombinant plantvirus vector or in a recombinant baculovirus vector. Such recombinantexpression constructs or vectors can be designed to include additionalelements, such as expression cassettes for expressing a gene of interest(e. g., an insecticidal protein).

The polynucleotide useful in compositions of this invention (i. e., thepolynucleotide of this invention that is topically applied to the plant)has at least one segment of 18 or more contiguous nucleotides with asequence of about 95% to about 100% identity with a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof. In anembodiment the polynucleotide that is topically applied to the plantincludes at least 18 contiguous nucleotides that are essentiallyidentical or complementary to a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ IDNOs:1-450. In some embodiments, the contiguous nucleotides have asequence of about 95%, about 96%, about 97%, about 98%, about 99%, orabout 100% identity with the segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ ID NOs:1-450or the DNA complement thereof. In some embodiments the contiguousnucleotides are exactly (100%) identical to a segment of equivalentlength of a DNA having a sequence selected from the group consisting ofSEQ ID NOs:1-450 or the DNA complement thereof. In some embodiments, thepolynucleotide has an overall sequence of about 95%, about 96%, about97%, about 98%, about 99%, or about 100% identity with a segment of aDNA having a sequence selected from the group consisting of SEQ IDNOs:1-450 or the DNA complement thereof.

The polynucleotide useful in compositions of this invention (i. e., thepolynucleotide of this invention that is topically applied to the plant)includes at least 18 contiguous nucleotides with a sequence of about 95%to about 100% identity with a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ ID NOs:1-450or the DNA complement thereof. The contiguous nucleotides number atleast 18, e. g., between 18-24, or between 18-28, or between 20-30, orbetween 20-50, or between 20-100, or between 50-100, or between 100-250,or between 100-500, or between 200-1000, or between 500-2000, or evengreater, for example, up to the entire length of an open reading frameor up to the entire length of a gene or nucleotide sequence to besuppressed. The contiguous nucleotides can number more than 18, e. g.,19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or greater than 30, e.g., about 35, about 40, about 45, about 50, about 55, about 60, about65, about 70, about 75, about 80, about 85, about 90, about 95, about100, about 110, about 120, about 130, about 140, about 150, about 160,about 170, about 180, about 190, about 200, about 210, about 220, about230, about 240, about 250, about 260, about 270, about 280, about 290,about 300, or greater than 300.

The topically applied polynucleotide is generally designed to suppressone or more genes (“target genes”). Such target genes can include codingor non-coding sequence or both. In specific embodiments, thepolynucleotide is designed to suppress one or more target genes, whereeach target gene has a DNA sequence selected from the group consistingof SEQ ID NOs:1-450. In various embodiments, the topically appliedpolynucleotide is designed to suppress one or more genes, where eachgene has a sequence selected from the group consisting of SEQ IDNOs:1-450, and can be designed to suppress multiple genes from thisgroup, or to target different regions of one or more of these genes. Inan embodiment, the topically applied polynucleotide includes multiplesections or segments each of which includes at least 18 contiguousnucleotides with a sequence of about 95% to about 100% identity with asegment of equivalent length of a DNA having a sequence selected fromthe group consisting of SEQ ID NOs:1-450 or the DNA complement thereof.In such cases, each section can be identical or different in size or insequence, and can be sense or anti-sense relative to the target gene.For example, in one embodiment the topically applied polynucleotide caninclude multiple sections in tandem or repetitive arrangements, whereineach section includes at least 18 contiguous nucleotides with a sequenceof about 95% to about 100% identity with a segment of equivalent lengthof a DNA having a sequence selected from the group consisting of SEQ IDNOs:1-450 or the DNA complement thereof; “spacer” nucleotides which donot correspond to a target gene can optionally be used in between thesections.

The total length of the topically applied polynucleotide can be greaterthan 18 contiguous nucleotides, and can include nucleotides in additionto the contiguous nucleotides having the sequence of about 95% to about100% identity with a segment of equivalent length of a DNA having asequence selected from the group consisting of SEQ ID NOs:1-450 or theDNA complement thereof. In other words, the total length of thetopically applied polynucleotide can be greater than the length of thesection or segment of the polynucleotide designed to suppress one ormore target genes, where each target gene has a DNA sequence selectedfrom the group consisting of SEQ ID NOs:1-450. For example, thetopically applied polynucleotide can have nucleotides flanking the“active” segment of at least 18 contiguous nucleotides that suppressesthe target gene, or include “spacer” nucleotides between activesegments, or can have additional nucleotides at the 5′ end, or at the 3′end, or at both the 5′ and 3′ ends. In an embodiment, the topicallyapplied polynucleotide can include additional nucleotides that providestabilizing secondary structure.

In a related aspect, this invention is directed to the plant havingimproved resistance to a Diabrotica species infestation, provided bythis method which includes topically applying to the plant a compositionincluding at least one polynucleotide having at least one segment of 18or more contiguous nucleotides with a sequence of about 95% to about100% identity with a segment of equivalent length of a DNA having asequence selected from the group consisting of SEQ ID NOs:1-450 or theDNA complement thereof, whereby the plant treated with thepolynucleotide composition exhibits improved resistance to a Diabroticaspecies infestation, relative to an untreated plant. In yet anotheraspect, this invention is directed to seed (especially transgenicprogeny seed) produced by the plant having improved resistance to aDiabrotica species infestation, as provided by this method. Alsocontemplated is a commodity product produced by the plant havingimproved resistance to a Diabrotica species infestation, as provided bythis method, and a commodity product produced from the transgenicprogeny seed of such a plant.

Compositions for Controlling Diabrotica Species

Another aspect of this invention provides a composition for controllinga Diabrotica species including at least one recombinant polynucleotideincluding at least 18 contiguous nucleotides that are essentiallyidentical or complementary to a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ IDNOs:1-450. In an embodiment the recombinant polynucleotide has at leastone segment of 18 or more contiguous nucleotides with a sequence ofabout 95% to about 100% identity with a segment of equivalent length ofa DNA having a sequence selected from the group consisting of SEQ IDNOs:1-450 or the DNA complement thereof. In this context “controlling”includes inducement of a physiological or behavioural change such as,but not limited to, growth stunting, increased mortality, decrease inreproductive capacity, decrease in or cessation of feeding behavior ormovement, or decrease in or cessation of metamorphosis stagedevelopment.

In various embodiments, the composition for controlling a Diabroticaspecies is in the form of at least one selected from the groupconsisting of a solid, liquid (including homogeneous mixtures such assolutions and non-homogeneous mixtures such as suspensions, colloids,micelles, and emulsions), powder, suspension, emulsion, spray,encapsulated or micro-encapsulation formulation, in or on microbeads orother carrier particulates, in a film or coating, or on or within amatrix. Suitable binders, inert carriers, surfactants, and the like canbe included in the composition for controlling a Diabrotica species, asis known to one skilled in formulation of pesticides and seedtreatments. In embodiments, the composition for controlling a Diabroticaspecies further includes one or more components selected from the groupconsisting of a carrier agent, a surfactant, an organosilicone, apolynucleotide herbicidal molecule, a non-polynucleotide herbicidalmolecule, a non-polynucleotide pesticide, a safener, and an insectgrowth regulator. In one embodiment the composition for controlling aDiabrotica species further includes a nonionic organosilicone surfactantsuch as Silwet, e. g., Silwet® L-77 surfactant having CAS Number27306-78-1 and EPA Number: CAL.REG.NO. 5905-50073-AA, currentlyavailable from Momentive Performance Materials, Albany, N.Y. Inembodiments, the composition for controlling a Diabrotica speciesfurther includes at least one pesticidal agent selected from the groupconsisting of a patatin, a plant lectin, a phytoecdysteroid, aphytoecdysteroid, a Bacillus thuringiensis insecticidal protein, aXenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, aBacillus laterosporous insecticidal protein, and a Bacillus sphearicusinsecticidal protein.

It is anticipated that the combination of certain recombinantpolynucleotides of this invention (e. g., the polynucleotide triggersdescribed in the working Examples) with one or more non-polynucleotidepesticidal agents will result in a synergetic improvement in preventionor control of Diabrotica species infestations, when compared to theeffect obtained with the recombinant polynucleotide alone or thenon-polynucleotide pesticidal agent alone. In an embodiment, acomposition containing one or more recombinant polynucleotides of thisinvention and one or more non-polynucleotide pesticidal agent selectedfrom the group consisting of a patatin, a plant lectin, aphytoecdysteroid, a Bacillus thuringiensis insecticidal protein, aXenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, aBacillus laterosporous insecticidal protein, and a Bacillus sphearicusinsecticidal protein, is found to effect synergistically improvedprevention or control of Diabrotica species infestations.

The composition for controlling a Diabrotica species can be provided fordietary uptake by the Diabrotica species by applying the composition toa plant or surface subject to infestation by the Diabrotica species, forexample by spraying, dusting, or coating the plant, or by application ofa soil drench, or by providing in an artificial diet. The compositionfor controlling a Diabrotica species can be provided for dietary uptakeby the Diabrotica species in an artificial diet formulated to meet theparticular nutritional requirements for maintaining the Diabroticaspecies, wherein the artificial diet is supplemented with some amount ofthe recombinant polynucleotide obtained from a separate source such aschemical synthesis or purified from a microbial fermentation; thisembodiment can be useful, e. g., for determining the timing and amountsof effective polynucleotide treatment regimes. In some embodiments thecomposition for controlling a Diabrotica species is provided for dietaryuptake by the Diabrotica species in the form of a plant cell or in plantcell components, or in a microorganism (such as a bacterium or a yeast)or a microbial fermentation product, or in a synthetic diet. In oneembodiment the composition for controlling a Diabrotica species isprovided in the form of bait that is ingested by the Diabrotica species.The composition for controlling a Diabrotica species can be provided fordietary uptake by the Diabrotica species in the form of a seedtreatment.

In various embodiments, the composition for controlling a Diabroticaspecies includes a microbial cell or is produced in a microorganism. Forexample, the composition for controlling a Diabrotica species caninclude or can be produced in bacteria or yeast cells. In similarembodiments the composition for controlling a Diabrotica speciesincludes a transgenic plant cell or is produced in a plant cell (forexample a plant cell transiently expressing the polynucleotide); suchplant cells can be cells in an plant or cells grown in tissue culture orin cell suspension.

In various embodiments, the Diabrotica species to be controlled is atleast one selected from the group consisting of Diabrotica balteata,Diabrotica barberi, Diabrotica beniensis, Diabrotica cristata,Diabrotica curvipustulata, Diabrotica dissimilis, Diabrotica elegantula,Diabrotica emorsitans, Diabrotica graminea, Diabrotica hispanolae,Diabrotica lemniscata, Diabrotica linsleyi, Diabrotica longicornis,Diabrotica milleri, Diabrotica nummularis, Diabrotica occlusa,Diabrotica porracea, Diabrotica scutellata, Diabrotica speciosa,Diabrotica tibialis, Diabrotica trifasciata, Diabrotica undecimpunctata,Diabrotica virgifera, and Diabrotica viridula. In specific embodiments,the Diabrotica species is at least one selected from the groupconsisting of Diabrotica virgifera virgifera (Western Corn Rootworm,WCR), Diabrotica undecimpunctata howardii (Southern Corn Rootworm, SCR),Diabrotica barberi (Northern Corn Rootworm, NCR), Diabrotica virgiferazeae (Mexican Corn Rootworm, MCR), Diabrotica balteata (Brazilian CornRootworm, BZR), or Brazilian Corn Rootworm complex (BCR) consisting ofDiabrotica viridula and Diabrotica speciosa.

In some embodiments the Diabrotica species to be controlled infests aplant. Of particular interest are embodiments wherein the plant is a rowcrop plant or a vegetable crop plant. Examples include a plant selectedfrom the group consisting of maize, cucumber, squash, soybeans, and drybeans. One row crop plant of interest is maize, and embodiments includethose wherein the plant is an ungerminated maize seed, or a maize plantin a vegetative stage (from emergence to tasseling stage, i. e., VE, V1,V2, V3, . . . , V(n), VT), or a maize plant in a reproductive stage (R1,R2, R3, R4, R5, R6). One embodiment includes maize plants in a field ofmaize.

The recombinant polynucleotide useful in compositions of this inventioncan be single-stranded (ss) or double-stranded (ds). “Double-stranded”refers to the base-pairing that occurs between sufficientlycomplementary, anti-parallel nucleic acid strands to form adouble-stranded nucleic acid structure, generally under physiologicallyrelevant conditions. Embodiments of the method include those wherein therecombinant polynucleotide is at least one selected from the groupconsisting of sense single-stranded DNA (ssDNA), sense single-strandedRNA (ssRNA), double-stranded RNA (dsRNA), double-stranded DNA (dsDNA), adouble-stranded DNA/RNA hybrid, anti-sense ssDNA, or anti-sense ssRNA; amixture of polynucleotides of any of these types can be used.

The recombinant polynucleotide of the composition for controlling aDiabrotica species includes at least 18 contiguous nucleotides that areessentially identical or complementary to a segment of equivalent lengthof a DNA having a sequence selected from the group consisting of SEQ IDNOs:1-450. In an embodiment the recombinant polynucleotide has at leastone segment of 18 or more contiguous nucleotides with a sequence ofabout 95% to about 100% identity with a segment of equivalent length ofa DNA having a sequence selected from the group consisting of SEQ IDNOs:1-450 or the DNA complement thereof In some embodiments, thecontiguous nucleotides have a sequence of about 95%, about 96%, about97%, about 98%, about 99%, or about 100% identity with the segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof. In someembodiments the contiguous nucleotides are exactly (100%) identical to asegment of equivalent length of a DNA having a sequence selected fromthe group consisting of SEQ ID NOs:1-450 or the DNA complement thereof.In some embodiments, the polynucleotide has an overall sequence of about95%, about 96%, about 97%, about 98%, about 99%, or about 100% identitywith a segment of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof.

Recombinant polynucleotides of use in the composition for controlling aDiabrotica species include at least 18 contiguous nucleotides with asequence of about 95% to about 100% identity with a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof. Thecontiguous nucleotides number at least 18, e. g., between 18-24, orbetween 18-28, or between 20-30, or between 20-50, or between 20-100, orbetween 50-100, or between 100-250, or between 100-500, or between200-1000, or between 500-2000, or even greater, for example, up to theentire length of an open reading frame or up to the entire length of agene or nucleotide sequence to be suppressed. The contiguous nucleotidescan number more than 18, e. g., 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, 30, or greater than 30, e. g., about 35, about 40, about 45, about50, about 55, about 60, about 65, about 70, about 75, about 80, about85, about 90, about 95, about 100, about 110, about 120, about 130,about 140, about 150, about 160, about 170, about 180, about 190, about200, about 210, about 220, about 230, about 240, about 250, about 260,about 270, about 280, about 290, about 300, or greater than 300.

The recombinant polynucleotide is generally designed to suppress one ormore genes (“target genes”). The term “gene” refers to any portion of anucleic acid that provides for expression of a transcript or encodes atranscript. A “gene” thus includes, but is not limited to, a promoterregion, 5′ untranslated regions, transcript encoding regions that caninclude intronic regions, and 3′ untranslated regions. Thus, the targetgenes can include coding or non-coding sequence or both. In specificembodiments, the polynucleotide is designed to suppress one or moretarget genes, where each target gene has a DNA sequence selected fromthe group consisting of SEQ ID NOs:1-450. In various embodiments, thepolynucleotide is designed to suppress one or more genes, where eachgene has a sequence selected from the group consisting of SEQ IDNOs:1-450, and can be designed to suppress multiple genes from thisgroup, or to target different regions of one or more of these genes. Inan embodiment, the polynucleotide includes multiple sections or segmentseach of which includes at least 18 contiguous nucleotides with asequence of about 95% to about 100% identity with a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof. In suchcases, each section can be identical or different in size or insequence, and can be sense or anti-sense relative to the target gene.For example, in one embodiment the polynucleotide can include multiplesections in tandem or repetitive arrangements, wherein each sectionincludes at least 18 contiguous nucleotides with a sequence of about 95%to about 100% identity with a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ ID NOs:1-450or the DNA complement thereof; “spacer” nucleotides which do notcorrespond to a target gene can optionally be used in between thesections.

The total length of the recombinant polynucleotide useful incompositions of this invention can be greater than 18 contiguousnucleotides, and can include nucleotides in addition to the contiguousnucleotides having the sequence of about 95% to about 100% identity witha segment of equivalent length of a DNA having a sequence selected fromthe group consisting of SEQ ID NOs:1-450 or the DNA complement thereof.In other words, the total length of the polynucleotide can be greaterthan the length of the section or segment of the polynucleotide designedto suppress one or more target genes, where each target gene has a DNAsequence selected from the group consisting of SEQ ID NOs:1-450. Forexample, the polynucleotide can have nucleotides flanking the “active”segment of at least 18 contiguous nucleotides that suppresses the targetgene, or include “spacer” nucleotides between active segments, or canhave additional nucleotides at the 5′ end, or at the 3′ end, or at boththe 5′ and 3′ ends. In an embodiment, the polynucleotide can includeadditional nucleotides that provide stabilizing secondary structure.

In various embodiments the recombinant polynucleotide useful incompositions of this invention consists of naturally occurringnucleotides, such as those which occur in DNA and RNA. In certainembodiments, the polynucleotide is a combination of ribonucleotides anddeoxyribonucleotides, for example, synthetic polynucleotides consistingmainly of ribonucleotides but with one or more terminaldeoxyribonucleotides or synthetic polynucleotides consisting mainly ofdeoxyribonucleotides but with one or more terminaldideoxyribonucleotides. In certain embodiments, the polynucleotideincludes non-canonical nucleotides such as inosine, thiouridine, orpseudouridine. In certain embodiments, the polynucleotide includeschemically modified nucleotides. Examples of chemically modifiedoligonucleotides or polynucleotides are well known in the art; see, forexample, U.S. Patent Publication 2011/0171287, U.S. Patent Publication2011/0171176, U.S. Patent Publication 2011/0152353, U.S. PatentPublication 2011/0152346, and U.S. Patent Publication 2011/0160082,which are herein incorporated by reference. Illustrative examplesinclude, but are not limited to, the naturally occurring phosphodiesterbackbone of an oligonucleotide or polynucleotide which can be partiallyor completely modified with phosphorothioate, phosphorodithioate, ormethylphosphonate internucleotide linkage modifications, modifiednucleoside bases or modified sugars can be used in oligonucleotide orpolynucleotide synthesis, and oligonucleotides or polynucleotides can belabeled with a fluorescent moiety (e. g., fluorescein or rhodamine) orother label (e. g., biotin).

The recombinant polynucleotide useful in compositions of this inventionis provided by suitable means known to one in the art. Embodimentsinclude those wherein the polynucleotide is chemically synthesized (e.g., by in vitro transcription, such as transcription using a T7polymerase or other polymerase), produced by expression in amicroorganism or in cell culture (such as plant or insect cells grown inculture), produced by expression in a plant cell, or produced bymicrobial fermentation.

In many embodiments the recombinant polynucleotide is provided as anisolated DNA or RNA fragment (not part of an expression construct, i.e., lacking additional elements such as a promoter or terminatorsequences). Such polynucleotides can be relatively short, such assingle- or double-stranded polynucleotides of between about 18 to about200 or about 300 nucleotides (for single-stranded polynucleotides) orbetween about 18 to about 200 or about 300 base-pairs (fordouble-stranded polynucleotides). Alternatively the polynucleotide canbe provided in more complex constructs, e. g., as part of a recombinantexpression construct, or included in a recombinant vector, for examplein a recombinant plant virus vector or in a recombinant baculovirusvector. Such recombinant expression constructs or vectors can bedesigned to include additional elements, such as expression cassettesfor expressing a gene of interest (e. g., an insecticidal protein).

Methods of Providing Plants Having Improved Resistance to DiabroticaSpecies Infestations, and the Plants and Seeds Thus Provided

Another aspect of this invention provides a method of providing a planthaving improved resistance to a Diabrotica species infestation includingexpressing in the plant at least one polynucleotide including at least18 contiguous nucleotides that are essentially identical orcomplementary to a segment of equivalent length of a DNA having asequence selected from the group consisting of SEQ ID NOs:1-450, wherebythe resulting plant has improved resistance to a Diabrotica species whencompared to a control plant in which the polynucleotide is notexpressed. In an embodiment the method includes expressing in the plantat least one polynucleotide including at least one segment of 18 or morecontiguous nucleotides with a sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof. By “expressing a polynucleotide in the plant” isgenerally meant “expressing an RNA transcript in the plant”. However,the polynucleotide expressed in the plant can also be DNA, e. g., a DNAproduced in the plant during genome replication.

The plant can be any plant that is subject to infestation by aDiabrotica species. Of particular interest are embodiments wherein theplant is a row crop plant or a vegetable crop plant. Examples include aplant selected from the group consisting of maize, cucumber, squash,soybeans, and dry beans. One row crop plant of interest is maize, andembodiments include those wherein the plant is an ungerminated maizeseed, or a maize plant in a vegetative stage (from emergence totasseling stage, i. e., VE, V1, V2, V3, . . . , V(n), VT), or a maizeplant in a reproductive stage (R1, R2, R3, R4, R5, R6). One embodimentincludes maize plants in a field of maize.

In various embodiments, the Diabrotica species is at least one selectedfrom the group consisting of Diabrotica balteata, Diabrotica barberi,Diabrotica beniensis, Diabrotica cristata, Diabrotica curvipustulata,Diabrotica dissimilis, Diabrotica elegantula, Diabrotica emorsitans,Diabrotica graminea, Diabrotica hispanolae, Diabrotica lemniscata,Diabrotica linsleyi, Diabrotica longicornis, Diabrotica milleri,Diabrotica nummularis, Diabrotica occlusa, Diabrotica porracea,Diabrotica scutellata, Diabrotica speciosa, Diabrotica tibialis,Diabrotica trifasciata, Diabrotica undecimpunctata, Diabroticavirgifera, and Diabrotica viridula. In specific embodiments, theDiabrotica species is at least one selected from the group consisting ofDiabrotica virgifera virgifera (Western Corn Rootworm, WCR), Diabroticaundecimpunctata howardii (Southern Corn Rootworm, SCR), Diabroticabarberi (Northern Corn Rootworm, NCR), Diabrotica virgifera zeae(Mexican Corn Rootworm, MCR), Diabrotica balteata (Brazilian CornRootworm, BZR), or Brazilian Corn Rootworm complex (BCR) consisting ofDiabrotica viridula and Diabrotica speciosa.

The method includes expressing at least one polynucleotide in a plant.In many embodiments, a first polynucleotide can be provided to a plantin the form of DNA (e. g., in the form of an isolated DNA molecule, oras an expression construct, or as a transformation vector), and thepolynucleotide expressed in the plant is a second polynucleotide (an RNAtranscript) in the plant. In an embodiment, the polynucleotide isexpressed in the plant by transgenic expression, i. e., by stablyintegrating the polynucleotide into the plant's genome from where it canbe expressed in a cell or cells of the plant. In an embodiment, a firstpolynucleotide (e. g., a recombinant DNA construct including a promoteroperably linked to DNA encoding an RNA silencing element for suppressinga target gene selected from the group consisting of the genes identifiedin Table 1) is stably integrated into the plant's genome from wheresecondarily produced polynucleotides (e. g., an RNA transcript includingthe RNA silencing element for suppressing the target gene) can beexpressed in a cell or cells of the plant. Methods of providing stablytransformed plant are provided in the section headed “Making and UsingTransgenic Plant Cells and Transgenic Plants”.

In another embodiment the polynucleotide of use in methods of thisinvention is expressed by transient expression. In such embodiments themethod can include a step of introducing a polynucleotide into the plantby routine techniques known in the art. For example, transientexpression can be accomplished by infiltration of a polynucleotidesolution using a needle-less syringe into a leaf of a plant.

In some embodiments where the polynucleotide of use in methods of thisinvention is expressed by transient expression, a first polynucleotideis provided to a plant in the form of RNA or DNA or both RNA and DNA,and a secondarily produced second polynucleotide is transientlyexpressed in the plant. In embodiments, the first polynucleotide is oneor more selected from: (a) a single-stranded RNA molecule (ssRNA), (b) asingle-stranded RNA molecule that self-hybridizes to form adouble-stranded RNA molecule, (c) a double-stranded RNA molecule(dsRNA), (d) a single-stranded DNA molecule (ssDNA), (e) asingle-stranded DNA molecule that self-hybridizes to form adouble-stranded DNA molecule, (f) a single-stranded DNA moleculeincluding a modified Pol III gene that is transcribed to an RNAmolecule, (g) a double-stranded DNA molecule (dsDNA), (h) adouble-stranded DNA molecule including a modified Pol III gene that istranscribed to an RNA molecule, and (i) a double-stranded, hybridizedRNA/DNA molecule, or combinations thereof. In embodiments, a firstpolynucleotide is introduced into the plant by topical application tothe plant of a polynucleotide-containing composition in a suitable form,e. g., as a solid, liquid (including homogeneous mixtures such assolutions and non-homogeneous mixtures such as suspensions, colloids,micelles, and emulsions), powder, suspension, emulsion, spray,encapsulated or micro-encapsulation formulation, in or on microbeads orother carrier particulates, in a film or coating, or on or within amatrix. Topical application of the polynucleotide-containing compositionto the plant can be in the form of a seed treatment. Suitable binders,inert carriers, surfactants, and the like can optionally be included inthe composition, as is known to one skilled in formulation of pesticidesand seed treatments. In embodiments, the polynucleotide-containingcomposition further includes one or more components selected from thegroup consisting of a carrier agent, a surfactant, an organosilicone, apolynucleotide herbicidal molecule, a non-polynucleotide herbicidalmolecule, a non-polynucleotide pesticide, a safener, and an insectgrowth regulator. In one embodiment the composition further includes anonionic organosilicone surfactant such as Silwet, e. g., Silwet® L-77surfactant having CAS Number 27306-78-1 and EPA Number: CAL.REG.NO.5905-50073-AA, currently available from Momentive Performance Materials,Albany, N.Y. In embodiments, the topically applied composition furtherincludes at least one pesticidal agent selected from the groupconsisting of a patatin, a plant lectin, a phytoecdysteroid, a Bacillusthuringiensis insecticidal protein, a Xenorhabdus insecticidal protein,a Photorhabdus insecticidal protein, a Bacillus laterosporousinsecticidal protein, and a Bacillus sphearicus insecticidal protein.Alternatively such additional components or pesticidal agents can beprovided separately, e. g., by separate topical application or bytransgenic expression in the plant. Alternatively the plant is topicallytreated with the polynucleotide-containing composition as well as with aseparate (preceding, following, or concurrent) application of asubstance that improves the efficacy of the polynucleotide-containingcomposition. For example, a plant can be sprayed with a first topicalapplication of a solution containing a nonionic organosiliconesurfactant such as Silwet, e. g., Silwet® L-77, followed by a secondtopical application of the polynucleotide-containing composition, orvice-versa.

It is anticipated that the combination of certain polynucleotides ofthis invention (e. g., the polynucleotide triggers described in theworking Examples) with one or more non-polynucleotide pesticidal agentswill result in a synergetic improvement in prevention or control ofDiabrotica species infestations, when compared to the effect obtainedwith the polynucleotide alone or the non-polynucleotide pesticidal agentalone. In an embodiment, a transgenic plant expressing one or morepolynucleotides of this invention and one or more genes encoding anon-polynucleotide pesticidal agent selected from the group consistingof a patatin, a plant lectin, a phytoecdysteroid, a Bacillusthuringiensis insecticidal protein, a Xenorhabdus insecticidal protein,a Photorhabdus insecticidal protein, a Bacillus laterosporousinsecticidal protein, and a Bacillus sphearicus insecticidal protein, isfound to exhibit synergistically improved resistance to Diabroticaspecies infestations.

In embodiments where the polynucleotide of use in methods of thisinvention is expressed by transient expression, a first polynucleotideis provided to a plant in the form of RNA or DNA or both RNA and DNA,and a secondarily produced second polynucleotide is transientlyexpressed in the plant; the site of application of the firstpolynucleotide need not be the same site where the second polynucleotideis transiently expressed. For example, a first polynucleotide can beprovided to a plant by topical application onto a leaf, or by injectioninto a stem, and the second polynucleotide can be transiently expressedelsewhere in the plant, e. g., in the roots or throughout the plant. Insome embodiments of the method, a composition including at least onepolynucleotide is topically applied to above-ground parts of the plant,e. g., sprayed or dusted onto leaves, stems, and flowering parts of theplant. In other embodiments, a composition including at least onepolynucleotide is topically applied to below-ground parts of the plant,such as to the roots, e. g., by means of a soil drench. In otherembodiments, a composition including at least one polynucleotide istopically applied to a seed that is grown into the plant having improvedresistance to a Diabrotica species infestation.

The polynucleotide of use in methods of this invention can besingle-stranded (ss) or double-stranded (ds). “Double-stranded” refersto the base-pairing that occurs between sufficiently complementary,anti-parallel nucleic acid strands to form a double-stranded nucleicacid structure, generally under physiologically relevant conditions.Embodiments of the method include those wherein the polynucleotide is atleast one selected from the group consisting of sense single-strandedDNA (ssDNA), sense single-stranded RNA (ssRNA), double-stranded RNA(dsRNA), double-stranded DNA (dsDNA), a double-stranded DNA/RNA hybrid,anti-sense ssDNA, or anti-sense ssRNA; a mixture of polynucleotides ofany of these types can be used.

In some embodiments a first polynucleotide (DNA or RNA or both) isprovided to a plant and a second polynucleotide having a sequencecorresponding to the first polynucleotide is subsequently expressed inthe plant. In such embodiments the polynucleotide expressed in the plantis an RNA transcript which can be ssRNA or dsRNA or both. In someembodiments where the polynucleotide is expressed by transientexpression, a first polynucleotide is provided to a plant in the form ofRNA or DNA or both RNA and DNA, and a secondarily produced secondpolynucleotide is transiently expressed in the plant. In embodiments,the first polynucleotide may be one or more of the following: (a) asingle-stranded RNA molecule (ssRNA), (b) a single-stranded RNA moleculethat self-hybridizes to form a double-stranded RNA molecule, (c) adouble-stranded RNA molecule (dsRNA), (d) a single-stranded DNA molecule(ssDNA), (e) a single-stranded DNA molecule that self-hybridizes to forma double-stranded DNA molecule, (f) a single-stranded DNA moleculeincluding a modified Pol III gene that is transcribed to an RNAmolecule, (g) a double-stranded DNA molecule (dsDNA), (h) adouble-stranded DNA molecule including a modified Pol III gene that istranscribed to an RNA molecule, and (i) a double-stranded, hybridizedRNA/DNA molecule, or combinations thereof. In various embodiments thefirst polynucleotide consists of naturally occurring nucleotides, suchas those which occur in DNA and RNA. In other embodiments the firstpolynucleotide is chemically modified, or includes chemically modifiednucleotides. The first polynucleotide is provided by suitable meansknown to one in the art. Embodiments include those wherein the firstpolynucleotide is chemically synthesized (e. g., by in vitrotranscription, such as transcription using a T7 polymerase or otherpolymerase), produced by expression in a microorganism or in cellculture (such as plant or insect cells grown in culture), produced byexpression in a plant cell, or produced by microbial fermentation. Thefirst polynucleotide can be provided as an RNA or DNA fragment.Alternatively the first polynucleotide can be provided in more complexconstructs, e. g., as part of a recombinant expression construct, orincluded in a recombinant vector, for example in a recombinant plantvirus vector or in a recombinant baculovirus vector; such recombinantexpression constructs or vectors can be designed to include additionalelements, such as expression cassettes for expressing a gene of interest(e. g., an insecticidal protein).

In many embodiments the polynucleotide expressed in the plant is anisolated RNA fragment and can be relatively short, such as single- ordouble-stranded RNAs of between about 18 to about 200 or about 300nucleotides (for single-stranded RNAs) or between about 18 to about 200or about 300 base-pairs (for double-stranded RNAs).

The polynucleotide expressed in the plant has at least one segment of 18or more contiguous nucleotides with a sequence of about 95% to about100% identity with a segment of equivalent length of a DNA having asequence selected from the group consisting of SEQ ID NOs:1-450 or theDNA complement thereof. In an embodiment the polynucleotide expressed inthe plant includes at least 18 contiguous nucleotides that areessentially identical or complementary to a segment of equivalent lengthof a DNA having a sequence selected from the group consisting of SEQ IDNOs:1-450. In some embodiments, the contiguous nucleotides have asequence of about 95%, about 96%, about 97%, about 98%, about 99%, orabout 100% identity with the segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ ID NOs:1-450or the DNA complement thereof. In some embodiments the contiguousnucleotides are exactly (100%) identical to a segment of equivalentlength of a DNA having a sequence selected from the group consisting ofSEQ ID NOs:1-450 or the DNA complement thereof. In some embodiments, thepolynucleotide has an overall sequence of about 95%, about 96%, about97%, about 98%, about 99%, or about 100% identity with a segment of aDNA having a sequence selected from the group consisting of SEQ IDNOs:1-450 or the DNA complement thereof.

The polynucleotide expressed in the plant includes at least 18contiguous nucleotides with a sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof. The contiguous nucleotides number at least 18, e.g., between 18-24, or between 18-28, or between 20-30, or between 20-50,or between 20-100, or between 50-100, or between 100-250, or between100-500, or between 200-1000, or between 500-2000, or even greater, forexample, up to the entire length of an open reading frame or up to theentire length of a gene or nucleotide sequence to be suppressed. Thecontiguous nucleotides can number more than 18, e. g., 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, or greater than 30, e. g., about 35,about 40, about 45, about 50, about 55, about 60, about 65, about 70,about 75, about 80, about 85, about 90, about 95, about 100, about 110,about 120, about 130, about 140, about 150, about 160, about 170, about180, about 190, about 200, about 210, about 220, about 230, about 240,about 250, about 260, about 270, about 280, about 290, about 300, orgreater than 300.

The polynucleotide expressed in the plant is generally designed tosuppress one or more genes (“target genes”). Such target genes caninclude coding or non-coding sequence or both. In specific embodiments,the polynucleotide expressed in the plant is designed to suppress one ormore target genes, where each target gene has a DNA sequence selectedfrom the group consisting of SEQ ID NOs:1-450. In various embodiments,the polynucleotide expressed in the plant is designed to suppress one ormore genes, where each gene has a sequence selected from the groupconsisting of SEQ ID NOs:1-450, and can be designed to suppress multiplegenes from this group, or to target different regions of one or more ofthese genes. In an embodiment, the polynucleotide expressed in the plantincludes multiple sections or segments each of which includes at least18 contiguous nucleotides with a sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof. In such cases, each section can be identical ordifferent in size or in sequence, and can be sense or anti-senserelative to the target gene. For example, in one embodiment thepolynucleotide expressed in the plant can include multiple sections intandem or repetitive arrangements, wherein each section includes atleast 18 contiguous nucleotides with a sequence of about 95% to about100% identity with a segment of equivalent length of a DNA having asequence selected from the group consisting of SEQ ID NOs:1-450 or theDNA complement thereof; “spacer” nucleotides which do not correspond toa target gene can optionally be used in between the sections.

The total length of the polynucleotide expressed in the plant can begreater than 18 contiguous nucleotides, and can include nucleotides inaddition to the contiguous nucleotides having the sequence of about 95%to about 100% identity with a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ ID NOs:1-450or the DNA complement thereof. In other words, the total length of thepolynucleotide expressed in the plant can be greater than the length ofthe section or segment of the polynucleotide designed to suppress one ormore target genes, where each target gene has a DNA sequence selectedfrom the group consisting of SEQ ID NOs:1-450. For example, thepolynucleotide expressed in the plant can have nucleotides flanking the“active” segment of at least 18 contiguous nucleotides that suppressesthe target gene, or include “spacer” nucleotides between activesegments, or can have additional nucleotides at the 5′ end, or at the 3′end, or at both the 5′ and 3′ ends. In an embodiment, the polynucleotideexpressed in the plant can include additional nucleotides that providestabilizing secondary structure.

In a related aspect, this invention is directed to the plant havingimproved resistance to a Diabrotica species infestation, provided byexpressing in the plant at least one polynucleotide including at least18 contiguous nucleotides that are essentially identical orcomplementary to a segment of equivalent length of a DNA having asequence selected from the group consisting of SEQ ID NOs:1-450, wherebythe resulting plant has improved resistance to a Diabrotica speciesinfestation when compared to a control plant in which the polynucleotideis not expressed. In a related aspect, this invention is directed to theplant having improved resistance to a Diabrotica species infestation,provided by expressing in the plant at least one polynucleotideincluding at least one segment of 18 or more contiguous nucleotides witha sequence of about 95% to about 100% identity with a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof, wherebythe resulting plant has improved resistance to a Diabrotica speciesinfestation when compared to a control plant in which the polynucleotideis not expressed. In yet another aspect, this invention is directed toseed (especially transgenic progeny seed) produced by the plant havingimproved resistance to a Diabrotica species infestation, as provided bythis method. Also contemplated is a commodity product produced by theplant having improved resistance to a Diabrotica species infestation, asprovided by this method, and a commodity product produced from thetransgenic progeny seed of such a plant.

Recombinant DNA Constructs for Controlling a Diabrotica Species

Another aspect of this invention provides a recombinant DNA constructincluding a heterologous promoter operably linked to DNA including atleast one segment of 18 or more contiguous nucleotides with a sequenceof about 95% to about 100% identity with a segment of equivalent lengthof a DNA having a sequence selected from the group consisting of SEQ IDNOs:1-450 or the DNA complement thereof. The recombinant DNA constructsare useful in providing a plant having improved resistance to aDiabrotica species infestation, e. g., by expressing in a plant atranscript of such a recombinant DNA construct. The recombinant DNAconstructs are also useful in the manufacture of polynucleotides usefulin making compositions that can be applied to a plant or surface in needof protection from a Diabrotica species infestation.

The recombinant DNA construct of this invention includes a heterologouspromoter operably linked to DNA including at least one segment of 18 ormore contiguous nucleotides with a sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof. In some embodiments, the segment of 18 or morecontiguous nucleotides has a sequence with about 95%, about 96%, about97%, about 98%, about 99%, or about 100% identity with the segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof. In someembodiments the contiguous nucleotides are exactly (100%) identical to asegment of equivalent length of a DNA having a sequence selected fromthe group consisting of SEQ ID NOs:1-450 or the DNA complement thereof.In some embodiments, the DNA has an overall sequence of about 95%, about96%, about 97%, about 98%, about 99%, or about 100% identity with a DNAhaving a sequence selected from the group consisting of SEQ ID NOs:1-450or the DNA complement thereof.

The recombinant DNA construct of this invention therefore includes aheterologous promoter operably linked to DNA including at least onesegment of 18 or more contiguous nucleotides designed to suppressexpression of a target gene having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof. Thecontiguous nucleotides of the segment number at least 18, e. g., between18-24, or between 18-28, or between 20-30, or between 20-50, or between20-100, or between 50-100, or between 100-250, or between 100-500, orbetween 200-1000, or between 500-2000, or even greater, for example, upto the entire length of an open reading frame or up to the entire lengthof a gene or nucleotide sequence to be suppressed. The contiguousnucleotides can number more than 18, e. g., 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, or greater than 30, e. g., about 35, about 40, about45, about 50, about 55, about 60, about 65, about 70, about 75, about80, about 85, about 90, about 95, about 100, about 110, about 120, about130, about 140, about 150, about 160, about 170, about 180, about 190,about 200, about 210, about 220, about 230, about 240, about 250, about260, about 270, about 280, about 290, about 300, or greater than 300.

The recombinant DNA construct of this invention includes a heterologouspromoter operably linked to DNA generally designed to suppress one ormore genes (“target genes”). Such target genes can include coding ornon-coding sequence or both. In specific embodiments, the recombinantDNA construct is designed to suppress one or more target genes, whereeach target gene has a DNA sequence selected from the group consistingof SEQ ID NOs:1-450. In various embodiments, the recombinant DNAconstruct is designed to suppress one or more genes, where each gene hasa sequence selected from the group consisting of SEQ ID NOs:1-450, andcan be designed to suppress multiple genes from this group, or to targetdifferent regions of one or more of these genes. In an embodiment, therecombinant DNA construct includes a heterologous promoter operablylinked to multiple sections or segments each of which includes at least18 contiguous nucleotides with a sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof. In such cases, each section can be identical ordifferent in size or in sequence, and can be sense or anti-senserelative to the target gene. For example, in one embodiment therecombinant DNA construct can include a heterologous promoter operablylinked to multiple sections in tandem or repetitive arrangements,wherein each section includes at least 18 contiguous nucleotides with asequence of about 95% to about 100% identity with a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof; “spacer”nucleotides which do not correspond to a target gene can optionally beused in between the sections.

The recombinant DNA construct of this invention includes a heterologouspromoter operably linked to DNA which can have a total length that isgreater than 18 contiguous nucleotides, and can include nucleotides inaddition to the segment of at least 18 contiguous nucleotides having thesequence of about 95% to about 100% identity with a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof. In otherwords, the total length of the DNA can be greater than the length of thesegment of the DNA designed to suppress one or more target genes, whereeach target gene has a DNA sequence selected from the group consistingof SEQ ID NOs:1-450. For example, the DNA can have nucleotides flankingthe “active” segment of at least 18 contiguous nucleotides thatsuppresses the target gene, or include “spacer” nucleotides betweenactive segments, or can have additional nucleotides at the 5′ end, or atthe 3′ end, or at both the 5′ and 3′ ends. In an embodiment, the DNA caninclude or encode additional nucleotides that provide stabilizingsecondary structure.

In recombinant DNA constructs of this invention, the heterologouspromoter is operably linked to DNA that encodes a transcript that can besingle-stranded (ss) or double-stranded (ds) or a combination of both.Embodiments of the method include those wherein the DNA encodes atranscript including sense single-stranded RNA (ssRNA), anti-sensessRNA, or double-stranded RNA (dsRNA), or a combination of any of these.

The recombinant DNA construct of this invention is provided by suitablemeans known to one in the art. Embodiments include those wherein therecombinant DNA construct is synthesized in vitro, produced byexpression in a microorganism or in cell culture (such as plant orinsect cells grown in culture), produced by expression in a plant cell,or produced by microbial fermentation.

The heterologous promoter of use in recombinant DNA constructs of thisinvention is selected from the group consisting of a promoter functionalin a plant, a promoter functional in a prokaryote, a promoter functionalin a fungal cell, and a baculovirus promoter. Non-limiting examples ofpromoters are described in the section headed “Promoters”.

In some embodiments, the recombinant DNA construct of this inventionincludes a second promoter also operably linked to the DNA. For example,the DNA including at least one segment of 18 or more contiguousnucleotides can be flanked by two promoters arranged so that thepromoters transcribe in opposite directions and in a convergent manner,yielding opposite-strand transcripts of the DNA that are complementaryto and capable of hybridizing with each other to form double-strandedRNA. In one embodiment, the DNA is located between two root-specificpromoters, which enable transcription of the DNA in opposite directions,resulting in the formation of dsRNA.

In some embodiments the recombinant DNA construct of this inventionincludes other DNA elements in addition to the heterologous promoteroperably linked to DNA including at least one segment of 18 or morecontiguous nucleotides with a sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof. Such DNA elements are known in the art, and includebut are not limited to introns, recombinase recognition sites, aptamersor ribozymes, additional and additional expression cassettes forexpressing coding sequences (e. g., to express a transgene such as aninsecticidal protein or selectable marker) or non-coding sequences (e.g., to express additional suppression elements). Inclusion of one ormore recognition sites for binding and cleavage by a small RNA (e. g.,by a miRNA or an siRNA that is expressed only in a particular cell ortissue) allows for more precise expression patterns in a plant, whereinthe expression of the recombinant DNA construct is suppressed where thesmall RNA is expressed.

In some embodiments, the recombinant DNA construct of this invention isprovided in a recombinant vector. By “recombinant vector” is meant arecombinant polynucleotide molecule that is used to transfer geneticinformation from one cell to another. Embodiments suitable to thisinvention include, but are not limited to, recombinant plasmids,recombinant cosmids, artificial chromosomes, and recombinant viralvectors such as recombinant plant virus vectors and recombinantbaculovirus vectors.

In some embodiments, the recombinant DNA construct of this invention isprovided in a plant chromosome or plastid, e. g., in a transgenic plantcell or a transgenic plant. Thus, also encompassed by this invention isa transgenic plant cell having in its genome the recombinant DNAconstruct, as well as a transgenic plant or partially transgenic plantincluding such a transgenic plant cell. Partially transgenic plantsinclude, e. g., a non-transgenic scion grafted onto a transgenicrootstock including the transgenic plant cell. In various embodimentsthe plant is a row crop plant or a vegetable crop plant. Of particularinterest are embodiments wherein the plant is a row crop plant or avegetable crop plant. Examples include a plant selected from the groupconsisting of maize, cucumber, squash, soybeans, and dry beans. One rowcrop plant of interest is maize, and embodiments include those whereinthe plant is an ungerminated maize seed, or a maize plant in avegetative stage (from emergence to tasseling stage, i. e., VE, V1, V2,V3, . . . , V(n), VT), or a maize plant in a reproductive stage (R1, R2,R3, R4, R5, R6). One embodiment includes maize plants in a field ofmaize. In yet another aspect, this invention is directed to seed(especially transgenic progeny seed) produced by the transgenic planthaving in its genome a recombinant DNA construct of this invention. Alsocontemplated is a commodity product produced by such a transgenic plant,and a commodity product produced from the transgenic progeny seed ofsuch a transgenic plant.

The recombinant DNA construct of this invention can be provided in acomposition for topical application to a surface of a plant or of aplant seed, or for topical application to any substrate needingprotection from a Diabrotica species infestation. Likewise, therecombinant DNA construct can be provided in a composition for topicalapplication to a Diabrotica species, or in a composition for ingestionby a Diabrotica species. In various embodiments, such compositionscontaining the recombinant DNA construct are provided in the form of atleast one selected from the group consisting of a solid, liquid(including homogeneous mixtures such as solutions and non-homogeneousmixtures such as suspensions, colloids, micelles, and emulsions),powder, suspension, emulsion, spray, encapsulated or micro-encapsulationformulation, in or on microbeads or other carrier particulates, in afilm or coating, or on or within a matrix. Suitable binders, inertcarriers, surfactants, and the like can be included in the compositioncontaining the recombinant DNA construct, as is known to one skilled informulation of pesticides and seed treatments. In embodiments, thecomposition containing the recombinant DNA construct further includesone or more components selected from the group consisting of a carrieragent, a surfactant, an organosilicone, a polynucleotide herbicidalmolecule, a non-polynucleotide herbicidal molecule, a non-polynucleotidepesticide, a safener, and an insect growth regulator. In one embodimentthe composition containing the recombinant DNA construct furtherincludes a nonionic organosilicone surfactant such as Silwet, e. g.,Silwet® L-77 surfactant having CAS Number 27306-78-1 and EPA Number:CAL.REG.NO. 5905-50073-AA, currently available from MomentivePerformance Materials, Albany, N.Y. In embodiments, the compositioncontaining the recombinant DNA construct further includes at least onepesticidal agent selected from the group consisting of a patatin, aplant lectin, a phytoecdysteroid, a phytoecdysteroid, a Bacillusthuringiensis insecticidal protein, a Xenorhabdus insecticidal protein,a Photorhabdus insecticidal protein, a Bacillus laterosporousinsecticidal protein, and a Bacillus sphearicus insecticidal protein.

It is anticipated that the combination of certain recombinant DNAconstructs of this invention (e. g., recombinant DNA constructsincluding the polynucleotide triggers described in the workingExamples), whether transgenically expressed or topically applied, withone or more non-polynucleotide pesticidal agents, whether transgenicallyexpressed or topically applied, will result in a synergetic improvementin prevention or control of Diabrotica species infestations, whencompared to the effect obtained with the recombinant DNA constructsalone or the non-polynucleotide pesticidal agent alone. In anembodiment, a recombinant DNA construct for expressing one or morepolynucleotides of this invention as well as one or more genes encodinga non-polynucleotide pesticidal agent selected from the group consistingof a patatin, a plant lectin, a phytoecdysteroid, a Bacillusthuringiensis insecticidal protein, a Xenorhabdus insecticidal protein,a Photorhabdus insecticidal protein, a Bacillus laterosporousinsecticidal protein, and a Bacillus sphearicus insecticidal protein, isfound to provide synergistically improved resistance to Diabroticaspecies infestations in plants expressing the recombinant DNA construct.

The composition containing the recombinant DNA construct of thisinvention can be provided for dietary uptake by a Diabrotica species byapplying the composition to a plant or surface subject to infestation bythe Diabrotica species, for example by spraying, dusting, or coating theplant, or by application of a soil drench, or by providing in anartificial diet. The composition containing the recombinant DNAconstruct can be provided for dietary uptake by a Diabrotica species inan artificial diet formulated to meet the particular nutritionalrequirements for maintaining the Diabrotica species, wherein theartificial diet is supplemented with some amount of the recombinant DNAconstruct obtained from a separate source such as in vitro synthesis orpurified from a microbial fermentation or other biological source; thisembodiment can be useful, e. g., for determining the timing and amountsof effective treatment regimes. In some embodiments the compositioncontaining the recombinant DNA construct is provided for dietary uptakeby the Diabrotica species in the form of a plant cell or in plant cellcomponents, or in a microorganism (such as a bacterium or a yeast) or amicrobial fermentation product, or in a synthetic diet. In oneembodiment the composition containing the recombinant DNA construct isprovided in the form of bait that is ingested by the Diabrotica species.The composition containing the recombinant DNA construct can be providedfor dietary uptake by the Diabrotica species in the form of a seedtreatment.

In various embodiments, the composition containing the recombinant DNAconstruct of this invention includes a microbial cell or is produced ina microorganism. For example, the composition for containing therecombinant DNA construct can include or can be produced in bacteria oryeast cells. In similar embodiments the composition containing therecombinant DNA construct includes a transgenic plant cell or isproduced in a plant cell (for example a plant cell transientlyexpressing the polynucleotide); such plant cells can be cells in anplant or cells grown in tissue culture or in cell suspension.

The recombinant DNA construct of this invention is particularly usefulfor making plants having improved resistance to a Diabrotica infestationas well as for making compositions for controlling a Diabrotica species.In various embodiments, the Diabrotica species to be controlled is atleast one selected from the group consisting of Diabrotica balteata,Diabrotica barberi, Diabrotica beniensis, Diabrotica cristata,Diabrotica curvipustulata, Diabrotica dissimilis, Diabrotica elegantula,Diabrotica emorsitans, Diabrotica graminea, Diabrotica hispanolae,Diabrotica lemniscata, Diabrotica linsleyi, Diabrotica longicornis,Diabrotica milleri, Diabrotica nummularis, Diabrotica occlusa,Diabrotica porracea, Diabrotica scutellata, Diabrotica speciosa,Diabrotica tibialis, Diabrotica trifasciata, Diabrotica undecimpunctata,Diabrotica virgifera, and Diabrotica viridula. In specific embodiments,the Diabrotica species is at least one selected from the groupconsisting of Diabrotica virgifera virgifera (Western Corn Rootworm,WCR), Diabrotica undecimpunctata howardii (Southern Corn Rootworm, SCR),Diabrotica barberi (Northern Corn Rootworm, NCR), Diabrotica virgiferazeae (Mexican Corn Rootworm, MCR), Diabrotica balteata (Brazilian CornRootworm, BZR), or Brazilian Corn Rootworm complex (BCR) consisting ofDiabrotica viridula and Diabrotica speciosa.

Transgenic Maize Plant Cells

Another aspect of this invention provides a plant cell expressing any ofthe recombinant DNA constructs of this invention. Such plant cellsinclude, for example: a transgenic maize plant cell expressing apolynucleotide comprising at least 18 contiguous nucleotides with asequence of about 95% to about 100% identity with a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof; atransgenic maize plant cell expressing a polynucleotide having at leastone segment of 18 or more contiguous nucleotides with a sequence ofabout 95% to about 100% identity with a segment of equivalent length ofa DNA having a sequence selected from the group consisting of SEQ IDNOs:1-450 or the DNA complement thereof; a transgenic maize plant cellexpressing a recombinant RNA comprising at least one silencing elementessentially identical or essentially complementary to a target gene ofsaid Diabrotica species larvae, wherein said target gene sequence isselected from the group consisting of SEQ ID NOs:1-450 or the complementthereof; a transgenic maize plant cell expressing a polynucleotidecomprising at least 18 contiguous nucleotides that are essentiallyidentical or complementary to a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ IDNOs:1-450; a transgenic maize plant cell expressing a recombinant DNAconstruct comprising a heterologous promoter operably linked to DNAcomprising at least one segment of 18 or more contiguous nucleotideswith a sequence of about 95% to about 100% identity with a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof; atransgenic maize plant cell expressing a recombinant DNA encoding RNAthat suppresses expression of a target gene in a Diabrotica species thatcontacts or ingests said RNA, wherein said RNA comprises at least onesilencing element complementary to said target gene, and wherein saidtarget gene sequence is selected from the group consisting of SEQ IDNOs:1-450 or the complement thereof; a transgenic maize plant cellexpressing a recombinant RNA molecule comprises at least 18 contiguousnucleotides that are essentially complementary to a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof; or atransgenic maize plant cell expressing a polynucleotide comprising atleast 18 contiguous nucleotides that are essentially identical orcomplementary to a segment of equivalent length of a DNA of a targetgene selected from the group consisting of the genes identified inTable 1. Such plant cells are useful in providing a plant havingimproved resistance to a Diabrotica species infestation when compared toa control plant lacking such plant cells. The plant cell can be anisolated plant cell, or a plant cell grown in culture, or a cell of anyplant that is subject to infestation by a Diabrotica species. Ofparticular interest are embodiments wherein the plant cell is a cell ofa row crop plant or a vegetable crop plant. Examples include a plantcell selected from the group consisting cells of maize, cucumber,squash, soybeans, and dry beans. Of particular interest is a cell ofmaize plants, and embodiments include those wherein the plant cell is acell of an ungerminated maize seed, or of a maize plant in a vegetativestage (from emergence to tasseling stage, i. e., VE, V1, V2, V3, . . . ,V(n), VT), or of a maize plant in a reproductive stage (R1, R2, R3, R4,R5, R6). One embodiment includes cells of maize plants in a field ofmaize.

In an embodiment, the recombinant DNA is stably integrated into theplant's genome from where it can be expressed in a cell or cells of theplant according to this invention. Methods of providing stablytransformed plants are provided in the section headed “Making and UsingTransgenic Plant Cells and Transgenic Plants”. Thus, one specific aspectof this invention provides a transgenic maize plant cell having in itsgenome a recombinant DNA encoding RNA that suppresses expression of atarget gene in a Diabrotica species that contacts or ingests the RNA,wherein the RNA includes at least one silencing element complementary tothe target gene, and wherein the target gene sequence is selected fromthe group consisting of SEQ ID NOs:1-450 or the complement thereof. Suchtransgenic maize plant cells are useful in providing a maize planthaving improved resistance to a Diabrotica species infestation whencompared to a control maize plant lacking such transgenic maize plantcells.

Where embodiments where the plant cell of this invention is used inproviding a plant exhibiting improved resistance to a Diabroticaspecies, the Diabrotica species is at least one selected from the groupconsisting of Diabrotica balteata, Diabrotica barberi, Diabroticabeniensis, Diabrotica cristata, Diabrotica curvipustulata, Diabroticadissimilis, Diabrotica elegantula, Diabrotica emorsitans, Diabroticagraminea, Diabrotica hispanolae, Diabrotica lemniscata, Diabroticalinsleyi, Diabrotica longicornis, Diabrotica milleri, Diabroticanummularis, Diabrotica occlusa, Diabrotica porracea, Diabroticascutellata, Diabrotica speciosa, Diabrotica tibialis, Diabroticatrifasciata, Diabrotica undecimpunctata, Diabrotica virgifera, andDiabrotica viridula. In specific embodiments, the Diabrotica species isat least one selected from the group consisting of Diabrotica virgiferavirgifera (Western Corn Rootworm, WCR), Diabrotica undecimpunctatahowardii (Southern Corn Rootworm, SCR), Diabrotica barberi (NorthernCorn Rootworm, NCR), Diabrotica virgifera zeae (Mexican Corn Rootworm,MCR), Diabrotica balteata (Brazilian Corn Rootworm, BZR), or BrazilianCorn Rootworm complex (BCR) consisting of Diabrotica viridula andDiabrotica speciosa.

One specific aspect of this invention provides a transgenic maize plantcell having in its genome a recombinant DNA encoding RNA that suppressesexpression of a target gene in a Diabrotica species that contacts oringests the RNA, wherein the RNA includes at least one silencing elementcomplementary to the target gene, and wherein the target gene sequenceis selected from the group consisting of SEQ ID NOs:1-450 or thecomplement thereof. In embodiments, the RNA element includes at least 18contiguous nucleotides with a sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof. In embodiments, the RNA element includes at least 18contiguous nucleotides capable of hybridizing in vivo or of hybridizingunder physiological conditions (e. g., such as physiological conditionsnormally found in the cells of a Diabrotica species) to a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450.

The RNA element useful in plant cells of this invention can includesense single-stranded RNA (ssRNA) or anti-sense ssRNA (where “sense” and“anti-sense” is in reference to the coding sequences of a target genesuch as those with a sequence selected from the group consisting of SEQID NOs:1-450), or can include double-stranded RNA (dsRNA) or anycombination of these. The RNA element useful in plant cells of thisinvention includes at least 18 contiguous nucleotides with a sequence ofabout 95% to about 100% identity with a segment of equivalent length ofa DNA having a sequence selected from the group consisting of SEQ IDNOs:1-450 or the DNA complement thereof. The contiguous nucleotidesnumber at least 18, e. g., between 18-24, or between 18-28, or between20-30, or between 20-50, or between 20-100, or between 50-100, orbetween 100-250, or between 100-500, or between 200-1000, or between500-2000, or even greater, for example, up to the entire length of anopen reading frame or up to the entire length of a gene or nucleotidesequence to be suppressed. The contiguous nucleotides can number morethan 18, e. g., 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, orgreater than 30, e. g., about 35, about 40, about 45, about 50, about55, about 60, about 65, about 70, about 75, about 80, about 85, about90, about 95, about 100, about 110, about 120, about 130, about 140,about 150, about 160, about 170, about 180, about 190, about 200, about210, about 220, about 230, about 240, about 250, about 260, about 270,about 280, about 290, about 300, or greater than 300.

The RNA element useful in plant cells of this invention is generallydesigned to suppress one or more genes (“target genes”). Such targetgenes can include coding or non-coding sequence or both. In specificembodiments, the RNA element is designed to suppress one or more targetgenes, where each target gene has a DNA sequence selected from the groupconsisting of SEQ ID NOs:1-450. In various embodiments, the RNA elementis designed to suppress one or more genes, where each gene has asequence selected from the group consisting of SEQ ID NOs:1-450, and canbe designed to suppress multiple genes from this group, or to targetdifferent regions of one or more of these genes. In an embodiment, theRNA element includes multiple sections or segments each of whichincludes at least 18 contiguous nucleotides with a sequence of about 95%to about 100% identity with a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ ID NOs:1-450or the DNA complement thereof. In such cases, each section can beidentical or different in size or in sequence, and can be sense oranti-sense relative to the target gene. For example, in one embodimentthe RNA element can include multiple sections in tandem or repetitivearrangements, wherein each section includes at least 18 contiguousnucleotides with a sequence of about 95% to about 100% identity with asegment of equivalent length of a DNA having a sequence selected fromthe group consisting of SEQ ID NOs:1-450 or the DNA complement thereof;“spacer” nucleotides which do not correspond to a target gene canoptionally be used in between the sections.

The total length of the transcript of the recombinant DNA constructuseful in plant cells of this invention can be greater than 18contiguous nucleotides, and can include nucleotides in addition to theRNA element having the sequence of about 95% to about 100% identity witha segment of equivalent length of a DNA having a sequence selected fromthe group consisting of SEQ ID NOs:1-450 or the DNA complement thereof.In other words, the total length of the transcript of the recombinantDNA construct can be greater than the length of the RNA element designedto suppress one or more target genes, where each target gene has a DNAsequence selected from the group consisting of SEQ ID NOs:1-450. Forexample, the transcript of the recombinant DNA construct can havenucleotides flanking the “active” RNA element of at least 18 contiguousnucleotides that suppresses the target gene, or include “spacer”nucleotides between active segments, or can have additional nucleotidesat the 5′ end, or at the 3′ end, or at both the 5′ and 3′ ends. In anembodiment, the transcript of the recombinant DNA construct can includeadditional nucleotides that provide stabilizing secondary structure.

The transcript of the recombinant DNA construct useful in plant cells ofthis invention has at least one RNA element of 18 or more contiguousnucleotides with a sequence of about 95% to about 100% identity with asegment of equivalent length of a DNA having a sequence selected fromthe group consisting of SEQ ID NOs:1-450 or the DNA complement thereof.In an embodiment the RNA element includes at least 18 contiguousnucleotides that are essentially identical or complementary to a segmentof equivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450. In some embodiments, the contiguousnucleotides have a sequence of about 95%, about 96%, about 97%, about98%, about 99%, or about 100% identity with the segment of equivalentlength of a DNA having a sequence selected from the group consisting ofSEQ ID NOs:1-450 or the DNA complement thereof. In some embodiments thecontiguous nucleotides are exactly (100%) identical to a segment ofequivalent length of a DNA having a sequence selected from the groupconsisting of SEQ ID NOs:1-450 or the DNA complement thereof. In someembodiments, the RNA element has an overall sequence of about 95%, about96%, about 97%, about 98%, about 99%, or about 100% identity with asegment of a DNA having a sequence selected from the group consisting ofSEQ ID NOs:1-450 or the DNA complement thereof.

In embodiments, the plant cell is further capable expressing additionalheterologous DNA sequences. For example, a transgenic maize plant cellcan have a genome that further includes recombinant DNA encoding atleast one pesticidal agent selected from the group consisting of apatatin, a plant lectin, a phytoecdysteroid, a phytoecdysteroid, aBacillus thuringiensis insecticidal protein, a Xenorhabdus insecticidalprotein, a Photorhabdus insecticidal protein, a Bacillus laterosporousinsecticidal protein, and a Bacillus sphearicus insecticidal protein.

In a related aspect, this invention is directed to a plant havingimproved resistance to a Diabrotica species infestation, such as atransgenic maize plant including a transgenic maize plant cellexpressing a recombinant DNA construct encoding an RNA element forsuppressing one or more target genes with a sequence selected from thegroup consisting of SEQ ID NOs:1-450. In yet another aspect, thisinvention is directed to seed (especially transgenic progeny seed)produced by the transgenic maize plant having improved resistance to aDiabrotica species infestation, as provided by this method. Alsocontemplated is a commodity product produced by the transgenic maizeplant having improved resistance to a Diabrotica species infestation, asprovided by this method, and a commodity product produced from thetransgenic progeny seed of such a transgenic maize plant.

Recombinant RNA Molecules for Controlling Diabrotica Species

Another aspect of this invention provides a recombinant RNA moleculethat causes mortality or stunting of growth in a Diabrotica species wheningested or contacted by the Diabrotica species, wherein the recombinantRNA molecule includes at least 18 contiguous nucleotides that areessentially complementary to a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ ID NOs:1-450or the DNA complement thereof. In one embodiment the recombinant RNAmolecule includes at least one segment of 18 or more contiguousnucleotides with a sequence of about 95% to about 100% identity with asegment of equivalent length of a DNA having a sequence selected fromthe group consisting of SEQ ID NOs:1-450 or the DNA complement thereof.In this context “controlling” includes inducement of a physiological orbehavioural change such as, but not limited to, growth stunting,increased mortality, decrease in reproductive capacity, decrease in orcessation of feeding behavior or movement, or decrease in or cessationof metamorphosis stage development. Generally the recombinant RNAmolecule has been isolated, that is, substantially purified from amixture such as from a fermentation or from an in vitro synthesismixture. Such a purified recombinant RNA molecule can of course becombined with other components to form compositions wherein therecombinant RNA molecule is an active agent, or can be combined withother nucleic acid elements, e. g., in a chimeric RNA molecule.

The recombinant RNA molecule of this invention is useful in themanufacture of compositions that can be applied to a plant or othersurface in need of protection from a Diabrotica species infestation. Therecombinant RNA molecule is useful in the manufacture of compositionsfor controlling a Diabrotica species that contacts or ingests such acomposition. In various embodiments, the Diabrotica species to becontrolled is at least one selected from the group consisting ofDiabrotica balteata, Diabrotica barberi, Diabrotica beniensis,Diabrotica cristata, Diabrotica curvipustulata, Diabrotica dissimilis,Diabrotica elegantula, Diabrotica emorsitans, Diabrotica graminea,Diabrotica hispanolae, Diabrotica lemniscata, Diabrotica linsleyi,Diabrotica longicornis, Diabrotica milleri, Diabrotica nummularis,Diabrotica occlusa, Diabrotica porracea, Diabrotica scutellata,Diabrotica speciosa, Diabrotica tibialis, Diabrotica trifasciata,Diabrotica undecimpunctata, Diabrotica virgifera, and Diabroticaviridula. In specific embodiments, the Diabrotica species is at leastone selected from the group consisting of Diabrotica virgifera virgifera(Western Corn Rootworm, WCR), Diabrotica undecimpunctata howardii(Southern Corn Rootworm, SCR), Diabrotica barberi (Northern CornRootworm, NCR), Diabrotica virgifera zeae (Mexican Corn Rootworm, MCR),Diabrotica balteata (Brazilian Corn Rootworm, BZR), or Brazilian CornRootworm complex (BCR) consisting of Diabrotica viridula and Diabroticaspeciosa.

Embodiments of the recombinant RNA molecule of this invention include atleast one segment of 18 or more contiguous nucleotides with a sequenceof about 95% to about 100% identity with a segment of equivalent lengthof a DNA having a sequence selected from the group consisting of SEQ IDNOs:1-450 or the DNA complement thereof. In some embodiments, thesegment of 18 or more contiguous nucleotides has a sequence with about95%, about 96%, about 97%, about 98%, about 99%, or about 100% identitywith the segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof. In some embodiments the contiguous nucleotides areexactly (100%) identical to a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ ID NOs:1-450or the DNA complement thereof. In some embodiments, the DNA has anoverall sequence of about 95%, about 96%, about 97%, about 98%, about99%, or about 100% identity with a DNA having a sequence selected fromthe group consisting of SEQ ID NOs:1-450 or the DNA complement thereof.

Embodiments of the recombinant RNA molecule of this invention include atleast one segment of 18 or more contiguous nucleotides designed tosuppress expression of a target gene having a sequence selected from thegroup consisting of SEQ ID NOs:1-450 or the DNA complement thereof. Thecontiguous nucleotides of the segment number at least 18, e. g., between18-24, or between 18-28, or between 20-30, or between 20-50, or between20-100, or between 50-100, or between 100-250, or between 100-500, orbetween 200-1000, or between 500-2000, or even greater, for example, upto the entire length of an open reading frame or up to the entire lengthof a gene or nucleotide sequence to be suppressed. The contiguousnucleotides can number more than 18, e. g., 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, or greater than 30, e. g., about 35, about 40, about45, about 50, about 55, about 60, about 65, about 70, about 75, about80, about 85, about 90, about 95, about 100, about 110, about 120, about130, about 140, about 150, about 160, about 170, about 180, about 190,about 200, about 210, about 220, about 230, about 240, about 250, about260, about 270, about 280, about 290, about 300, or greater than 300.

The recombinant RNA molecule of this invention is generally designed tosuppress one or more genes (“target genes”). Such target genes caninclude coding or non-coding sequence or both. In specific embodiments,the recombinant RNA molecule is designed to suppress one or more targetgenes, where each target gene has a DNA sequence selected from the groupconsisting of SEQ ID NOs:1-450. In various embodiments, the recombinantRNA molecule is designed to suppress one or more genes, where each genehas a sequence selected from the group consisting of SEQ ID NOs:1-450,and can be designed to suppress multiple genes from this group, or totarget different regions of one or more of these genes. Embodiments ofthe recombinant RNA molecule include at least one segment of 18 or morecontiguous nucleotides having a sequence designed to suppress one ormore genes, where each gene has a sequence selected from the groupconsisting of SEQ ID NOs:1-450. In an embodiment, the recombinant RNAmolecule includes multiple sections or segments each of which includesat least 18 contiguous nucleotides with a sequence of about 95% to about100% identity with a segment of equivalent length of a DNA having asequence selected from the group consisting of SEQ ID NOs:1-450 or theDNA complement thereof. In such cases, each section can be identical ordifferent in size or in sequence, and can be sense or anti-senserelative to the target gene. For example, in one embodiment therecombinant RNA molecule includes multiple sections in tandem orrepetitive arrangements, wherein each section includes at least 18contiguous nucleotides with a sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof; “spacer” nucleotides which do not correspond to atarget gene can optionally be used in between the sections.

The recombinant RNA molecule of this invention can have a total lengththat is greater than 18 contiguous nucleotides, and can includenucleotides in addition to the segment of at least 18 contiguousnucleotides having the sequence of about 95% to about 100% identity witha segment of equivalent length of a DNA having a sequence selected fromthe group consisting of SEQ ID NOs:1-450 or the DNA complement thereof.In other words, the total length of the recombinant RNA molecule can begreater than the length of the segment of the recombinant RNA moleculewhich is designed to suppress one or more target genes, where eachtarget gene has a DNA sequence selected from the group consisting of SEQID NOs:1-450. For example, the recombinant RNA molecule can havenucleotides flanking the “active” segment of at least 18 contiguousnucleotides that suppresses the target gene, or include “spacer”nucleotides between active segments, or can have additional nucleotidesat the 5′ end, or at the 3′ end, or at both the 5′ and 3′ ends. In anembodiment, the recombinant RNA molecule can include or encodeadditional nucleotides that provide stabilizing secondary structure.

The recombinant RNA molecule of this invention can be single-stranded(ss) or double-stranded (ds) or a combination of both. Embodiments ofthe recombinant RNA molecule include sense single-stranded RNA (ssRNA),anti-sense ssRNA, or double-stranded RNA (dsRNA), or a combination ofany of these.

The recombinant RNA molecule of this invention is provided by suitablemeans known to one in the art. Embodiments include those wherein therecombinant RNA molecule is synthesized in vitro, produced by expressionin a microorganism or in cell culture (such as plant or insect cellsgrown in culture), produced by expression in a plant cell, or producedby microbial fermentation.

In some embodiments the recombinant RNA molecule of this inventionincludes other RNA elements, such as RNA aptamers or ribozymes,additional non-coding RNA (e. g., additional suppression elements), orone or more recognition sites for binding and cleavage by a small RNA(e. g., by a miRNA or an siRNA that is expressed only in a particularcell or tissue).

The recombinant RNA molecule of this invention can be provided in acomposition for topical application to a surface of a plant or of aplant seed, or for topical application to any substrate needingprotection from a Diabrotica species infestation. Likewise, therecombinant RNA molecule can be provided in a composition for topicalapplication to a Diabrotica species, or in a composition for ingestionby a Diabrotica species. In various embodiments, such compositionscontaining the recombinant RNA molecule are provided in the form of atleast one selected from the group consisting of a solid, liquid(including homogeneous mixtures such as solutions and non-homogeneousmixtures such as suspensions, colloids, micelles, and emulsions),powder, suspension, emulsion, spray, encapsulated or micro-encapsulationformulation, in or on microbeads or other carrier particulates, in afilm or coating, or on or within a matrix. Suitable binders, inertcarriers, surfactants, and the like can included in the compositioncontaining the recombinant RNA molecule, as is known to one skilled informulation of pesticides and seed treatments. In embodiments, thecomposition containing the recombinant RNA molecule further includes oneor more components selected from the group consisting of a carrieragent, a surfactant, an organosilicone, a polynucleotide herbicidalmolecule, a non-polynucleotide herbicidal molecule, a non-polynucleotidepesticide, a safener, and an insect growth regulator. In one embodimentthe composition containing the recombinant RNA molecule further includesa nonionic organosilicone surfactant such as Silwet, e. g., Silwet® L-77surfactant having CAS Number 27306-78-1 and EPA Number: CAL.REG.NO.5905-50073-AA, currently available from Momentive Performance Materials,Albany, N.Y. In embodiments, the composition containing the recombinantRNA molecule further includes at least one pesticidal agent selectedfrom the group consisting of a patatin, a plant lectin, aphytoecdysteroid, a phytoecdysteroid, a Bacillus thuringiensisinsecticidal protein, a Xenorhabdus insecticidal protein, a Photorhabdusinsecticidal protein, a Bacillus laterosporous insecticidal protein, anda Bacillus sphearicus insecticidal protein.

The composition containing the recombinant RNA molecule of thisinvention can be provided for dietary uptake by a Diabrotica species byapplying the composition to a plant or surface subject to infestation bythe Diabrotica species, for example by spraying, dusting, or coating theplant, or by application of a soil drench, or by providing in anartificial diet. The composition containing the recombinant RNA moleculecan be provided for dietary uptake by a Diabrotica species in anartificial diet formulated to meet the particular nutritionalrequirements for maintaining the Diabrotica species, wherein theartificial diet is supplemented with some amount of the recombinant RNAmolecule obtained from a separate source such as in vitro synthesis orpurified from a microbial fermentation or other biological source; thisembodiment can be useful, e. g., for determining the timing and amountsof effective treatment regimes. In some embodiments the compositioncontaining the recombinant RNA molecule is provided for dietary uptakeby the Diabrotica species in the form of a plant cell or in plant cellcomponents, or in a microorganism (such as a bacterium or a yeast) or amicrobial fermentation product, or in a synthetic diet. In oneembodiment the composition containing the recombinant RNA molecule isprovided in the form of bait that is ingested by the Diabrotica species.The composition containing the recombinant RNA molecule can be providedfor dietary uptake by the Diabrotica species in the form of a seedtreatment.

In various embodiments, the composition containing the recombinant RNAmolecule of this invention includes a microbial cell or is produced in amicroorganism. For example, the composition for containing therecombinant RNA molecule can include or can be produced in bacteria oryeast cells. In similar embodiments the composition containing therecombinant RNA molecule includes a transgenic plant cell or is producedin a plant cell (for example a plant cell transiently expressing thepolynucleotide); such plant cells can be cells in an plant or cellsgrown in tissue culture or in cell suspension.

Methods of Providing Plants Having Improved Resistance to DiabroticaSpecies Infestations, and the Plants and Seeds Thus Provided

Another aspect of this invention provides a method of providing a planthaving improved resistance to a Diabrotica species infestation includingproviding to the plant at least one polynucleotide including at least 18contiguous nucleotides that are essentially identical or complementaryto a segment of equivalent length of a DNA of a target gene selectedfrom the group consisting of the genes identified in Table 1.Embodiments of these target genes are identified by name in Table 1 andinclude genes having a sequence selected from the group consisting ofSEQ ID NOs:1-450, as well as related genes including orthologues fromrelated insect species, for example related genes from other Diabroticaspecies, Tribolium species, or other related genera. Examples of suchtarget genes include the Tribolium castaneum genes listed in Table 1.

The plant can be any plant that is subject to infestation by aDiabrotica species. Of particular interest are embodiments wherein theplant is a row crop plant or a vegetable crop plant. Examples include aplant selected from the group consisting of maize, cucumber, squash,soybeans, and dry beans. One row crop plant of interest is maize, andembodiments include those wherein the plant is an ungerminated maizeseed, or a maize plant in a vegetative stage (from emergence totasseling stage, i. e., VE, V1, V2, V3, . . . , V(n), VT), or a maizeplant in a reproductive stage (R1, R2, R3, R4, R5, R6). One embodimentincludes maize plants in a field of maize.

In various embodiments, the Diabrotica species is at least one selectedfrom the group consisting of Diabrotica balteata, Diabrotica barberi,Diabrotica beniensis, Diabrotica cristata, Diabrotica curvipustulata,Diabrotica dissimilis, Diabrotica elegantula, Diabrotica emorsitans,Diabrotica graminea, Diabrotica hispanolae, Diabrotica lemniscata,Diabrotica linsleyi, Diabrotica longicornis, Diabrotica milleri,Diabrotica nummularis, Diabrotica occlusa, Diabrotica porracea,Diabrotica scutellata, Diabrotica speciosa, Diabrotica tibialis,Diabrotica trifasciata, Diabrotica undecimpunctata, Diabroticavirgifera, and Diabrotica viridula. In specific embodiments, theDiabrotica species is at least one selected from the group consisting ofDiabrotica virgifera virgifera (Western Corn Rootworm, WCR), Diabroticaundecimpunctata howardii (Southern Corn Rootworm, SCR), Diabroticabarberi (Northern Corn Rootworm, NCR), Diabrotica virgifera zeae(Mexican Corn Rootworm, MCR), Diabrotica balteata (Brazilian CornRootworm, BZR), or Brazilian Corn Rootworm complex (BCR) consisting ofDiabrotica viridula and Diabrotica speciosa.

In one embodiment the method includes topically applying to the plant acomposition including at least one polynucleotide including at least 18contiguous nucleotides that are essentially identical or complementaryto a segment of equivalent length of a DNA of a target gene selectedfrom the group consisting of the genes identified in Table 1, wherebythe plant treated with the polynucleotide composition exhibits improvedresistance to a Diabrotica species infestation, relative to an untreatedplant.

By “topical application” is meant application to the surface or exteriorof an object, such as the surface or exterior of a plant, such asapplication to the surfaces of a plant part such as a leaf, stem,flower, fruit, shoot, root, seed, tuber, flowers, anthers, or pollen, orapplication to an entire plant, or to the above-ground or below-groundportions of a plant. Topical application can be carried out onnon-living surfaces, such as application to soil, or to a surface ormatrix by which a Diabrotica insect can come in contact with thepolynucleotide. In various embodiments of the method, the compositionincluding at least one polynucleotide is topically applied to the plantin a suitable form, e. g., as a solid, liquid (including homogeneousmixtures such as solutions and non-homogeneous mixtures such assuspensions, colloids, micelles, and emulsions), powder, suspension,emulsion, spray, encapsulated or micro-encapsulation formulation, in oron microbeads or other carrier particulates, in a film or coating, or onor within a matrix. Topical application of the polynucleotide-containingcomposition to the plant can be in the form of a seed treatment.Suitable binders, inert carriers, surfactants, and the like canoptionally be included in the composition, as is known to one skilled informulation of pesticides and seed treatments. In one embodiment thepolynucleotide-containing composition can be ingested or otherwiseabsorbed internally by the Diabrotica species. For example, thepolynucleotide-containing composition can be in the form of bait. Inembodiments, the polynucleotide-containing composition further includesone or more components selected from the group consisting of a carrieragent, a surfactant, an organosilicone, a polynucleotide herbicidalmolecule, a non-polynucleotide herbicidal molecule, a non-polynucleotidepesticide, a safener, and an insect growth regulator. In one embodimentthe composition further includes a nonionic organosilicone surfactantsuch as Silwet, e. g., Silwet® L-77 surfactant having CAS Number27306-78-1 and EPA Number: CAL.REG.NO. 5905-50073-AA, currentlyavailable from Momentive Performance Materials, Albany, N.Y. Inembodiments, the topically applied composition further includes at leastone pesticidal agent selected from the group consisting of a patatin, aplant lectin, a phytoecdysteroid, a Bacillus thuringiensis insecticidalprotein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidalprotein, a Bacillus laterosporous insecticidal protein, and a Bacillussphearicus insecticidal protein. Alternatively such additionalcomponents or pesticidal agents can be provided separately, e. g., byseparate topical application or by transgenic expression in the plant.Alternatively the plant is topically treated with thepolynucleotide-containing composition as well as with a separate(preceding, following, or concurrent) application of a substance thatimproves the efficacy of the polynucleotide-containing composition. Forexample, a plant can be sprayed with a first topical application of asolution containing a nonionic organosilicone surfactant such as Silwet,e. g., Silwet® L-77, followed by a second topical application of thepolynucleotide-containing composition, or vice-versa.

It is anticipated that the combination of certain polynucleotides ofthis invention (e. g., the polynucleotide triggers described in theworking Examples) with one or more non-polynucleotide pesticidal agentswill result in a synergetic improvement in prevention or control ofDiabrotica species infestations, when compared to the effect obtainedwith the polynucleotide alone or the non-polynucleotide pesticidal agentalone. In an embodiment, a composition containing one or morepolynucleotides of this invention and one or more non-polynucleotidepesticidal agent selected from the group consisting of a patatin, aplant lectin, a phytoecdysteroid, a Bacillus thuringiensis insecticidalprotein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidalprotein, a Bacillus laterosporous insecticidal protein, and a Bacillussphearicus insecticidal protein, is found to effect synergisticallyimproved prevention or control of Diabrotica species infestations whentopically applied to a plant.

In some embodiments of the method of this invention, the compositionincluding at least one polynucleotide is topically applied toabove-ground parts of the plant, e. g., sprayed or dusted onto leaves,stems, and flowering parts of the plant. In other embodiments, thecomposition including at least one polynucleotide is topically appliedto below-ground parts of the plant, such as to the roots, e. g., bymeans of a soil drench. In other embodiments, the composition includingat least one polynucleotide is topically applied to a seed that is growninto the plant.

In embodiments, the method of this invention includes topically applyingto the plant a composition including at least one polynucleotideincluding at least 18 contiguous nucleotides that are essentiallyidentical or complementary to a segment of equivalent length of a DNA ofa target gene selected from the group consisting of the genes identifiedin Table 1. The polynucleotide topically applied to the plant can besingle-stranded (ss) or double-stranded (ds). “Double-stranded” refersto the base-pairing that occurs between sufficiently complementary,anti-parallel nucleic acid strands to form a double-stranded nucleicacid structure, generally under physiologically relevant conditions.Embodiments of the method include those wherein the polynucleotidetopically applied to the plant is at least one selected from the groupconsisting of sense single-stranded DNA (ssDNA), sense single-strandedRNA (ssRNA), double-stranded RNA (dsRNA), double-stranded DNA (dsDNA), adouble-stranded DNA/RNA hybrid, anti-sense ssDNA, or anti-sense ssRNA; amixture of polynucleotides of any of these types can be used.

In various embodiments of this invention the polynucleotide topicallyapplied to the plant consists of naturally occurring nucleotides, suchas those which occur in DNA and RNA. In certain embodiments, thepolynucleotide is a combination of ribonucleotides anddeoxyribonucleotides, for example, synthetic polynucleotides consistingmainly of ribonucleotides but with one or more terminaldeoxyribonucleotides or synthetic polynucleotides consisting mainly ofdeoxyribonucleotides but with one or more terminaldideoxyribonucleotides. In certain embodiments, the polynucleotideincludes non-canonical nucleotides such as inosine, thiouridine, orpseudouridine. In certain embodiments, the polynucleotide includeschemically modified nucleotides. Examples of chemically modifiedoligonucleotides or polynucleotides are well known in the art; see, forexample, U.S. Patent Publication 2011/0171287, U.S. Patent Publication2011/0171176, U.S. Patent Publication 2011/0152353, U.S. PatentPublication 2011/0152346, and U.S. Patent Publication 2011/0160082,which are herein incorporated by reference. Illustrative examplesinclude, but are not limited to, the naturally occurring phosphodiesterbackbone of an oligonucleotide or polynucleotide which can be partiallyor completely modified with phosphorothioate, phosphorodithioate, ormethylphosphonate internucleotide linkage modifications, modifiednucleoside bases or modified sugars can be used in oligonucleotide orpolynucleotide synthesis, and oligonucleotides or polynucleotides can belabeled with a fluorescent moiety (e. g., fluorescein or rhodamine) orother label (e. g., biotin).

The polynucleotide topically applied to the plant is provided bysuitable means known to one in the art. Embodiments include thosewherein the polynucleotide is chemically synthesized (e. g., by in vitrotranscription, such as transcription using a T7 polymerase or otherpolymerase), produced by expression in a microorganism or in cellculture (such as plant or insect cells grown in culture), produced byexpression in a plant cell, or produced by microbial fermentation.

In many embodiments of this invention the polynucleotide topicallyapplied to the plant is provided as an isolated DNA or RNA fragment (notpart of an expression construct, i. e., lacking additional elements suchas a promoter or terminator sequences). Such polynucleotides can berelatively short, such as single- or double-stranded polynucleotides ofbetween about 18 to about 200 or about 300 nucleotides (forsingle-stranded polynucleotides) or between about 18 to about 200 orabout 300 base-pairs (for double-stranded polynucleotides).Alternatively the polynucleotide can be provided in more complexconstructs, e. g., as part of a recombinant expression construct, orincluded in a recombinant vector, for example in a recombinant plantvirus vector or in a recombinant baculovirus vector. Such recombinantexpression constructs or vectors can be designed to include additionalelements, such as expression cassettes for expressing a gene of interest(e. g., an insecticidal protein).

The polynucleotide topically applied to the plant has at least onesegment of 18 or more contiguous nucleotides that are essentiallyidentical or complementary to a segment of equivalent length of a DNA ofa target gene selected from the group consisting of the genes identifiedin Table 1, or that have a sequence of about 95% to about 100% identitywith a segment of equivalent length of a DNA of a target gene selectedfrom the group consisting of the genes identified in Table 1. In anembodiment the polynucleotide topically applied to the plant includes atleast 18 contiguous nucleotides that are essentially identical orcomplementary to a segment of equivalent length of a DNA of a targetgene selected from the group consisting of the genes identified inTable 1. In some embodiments, the contiguous nucleotides have a sequenceof about 95%, about 96%, about 97%, about 98%, about 99%, or about 100%identity or complementarity with the segment of equivalent length of aDNA of a target gene selected from the group consisting of the genesidentified in Table 1. In some embodiments the contiguous nucleotidesare exactly (100%) identical or complementary to a segment of equivalentlength of a DNA of a target gene selected from the group consisting ofthe genes identified in Table 1. In some embodiments, the polynucleotidehas an overall sequence of about 95%, about 96%, about 97%, about 98%,about 99%, or about 100% identity or complementarity with a segment of aDNA of a target gene selected from the group consisting of the genesidentified in Table 1.

The polynucleotide topically applied to the plant includes at least 18contiguous nucleotides with a sequence of about 95% to about 100%identity or complementarity with a segment of equivalent length of a DNAof a target gene selected from the group consisting of the genesidentified in Table 1. The contiguous nucleotides number at least 18, e.g., between 18-24, or between 18-28, or between 20-30, or between 20-50,or between 20-100, or between 50-100, or between 100-250, or between100-500, or between 200-1000, or between 500-2000, or even greater, forexample, up to the entire length of an open reading frame or up to theentire length of a gene or nucleotide sequence to be suppressed. Thecontiguous nucleotides can number more than 18, e. g., 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, or greater than 30, e. g., about 35,about 40, about 45, about 50, about 55, about 60, about 65, about 70,about 75, about 80, about 85, about 90, about 95, about 100, about 110,about 120, about 130, about 140, about 150, about 160, about 170, about180, about 190, about 200, about 210, about 220, about 230, about 240,about 250, about 260, about 270, about 280, about 290, about 300, orgreater than 300.

The polynucleotide topically applied to the plant is generally designedto suppress one or more genes (“target genes”). Such target genes caninclude coding or non-coding sequence or both. In specific embodiments,the polynucleotide is designed to suppress one or more target genesselected from the group consisting of the genes identified in Table 1.In embodiments, each target gene has a DNA sequence selected from thegroup consisting of SEQ ID NOs:1-450. In various embodiments, thepolynucleotide topically applied to the plant is designed to suppressone or more genes, where each gene is selected from the group consistingof the genes identified in Table 1, and can be designed to suppressmultiple genes from this group, or to target different regions of one ormore of these genes. In an embodiment, the polynucleotide topicallyapplied to the plant includes multiple sections or segments each ofwhich includes at least 18 contiguous nucleotides with a sequence ofabout 95% to about 100% identity or complementarity with a segment ofequivalent length of a DNA of a target gene selected from the groupconsisting of the genes identified in Table 1. In such cases, eachsection can be identical or different in size or in sequence, and can besense or anti-sense relative to the target gene. For example, in oneembodiment the polynucleotide topically applied to the plant can includemultiple sections in tandem or repetitive arrangements, wherein eachsection includes at least 18 contiguous nucleotides with a sequence ofabout 95% to about 100% identity or complementarity with a segment ofequivalent length of a DNA of a target gene selected from the groupconsisting of the genes identified in Table 1; “spacer” nucleotideswhich do not correspond to a target gene can optionally be used inbetween the sections.

The total length of the polynucleotide topically applied to the plantcan be greater than 18 contiguous nucleotides, and can includenucleotides in addition to the contiguous nucleotides having thesequence of about 95% to about 100% identity or complementarity with asegment of equivalent length of a DNA of a target gene selected from thegroup consisting of the genes identified in Table 1. In other words, thetotal length of the polynucleotide topically applied to the plant can begreater than the length of the section or segment of the polynucleotidedesigned to suppress one or more target genes, where each target gene isselected from the group consisting of the genes identified in Table 1.For example, the polynucleotide topically applied to the plant can havenucleotides flanking the “active” segment of at least 18 contiguousnucleotides that suppresses the target gene, or include “spacer”nucleotides between active segments, or can have additional nucleotidesat the 5′ end, or at the 3′ end, or at both the 5′ and 3′ ends. In anembodiment, the polynucleotide topically applied to the plant caninclude additional nucleotides that provide stabilizing secondarystructure.

In a related aspect, this invention is directed to the plant havingimproved resistance to a Diabrotica species infestation, provided bythis method which includes topically applying to the plant a compositionincluding at least one polynucleotide including at least 18 contiguousnucleotides that are essentially identical or complementary to a segmentof equivalent length of a DNA of a target gene selected from the groupconsisting of the genes identified in Table 1, whereby the plant treatedwith the polynucleotide composition exhibits improved resistance to aDiabrotica species infestation, relative to an untreated plant. In yetanother aspect, this invention is directed to seed (especiallytransgenic progeny seed) produced by the plant having improvedresistance to a Diabrotica species infestation, as provided by thismethod. Also contemplated is a commodity product produced by the planthaving improved resistance to a Diabrotica species infestation, asprovided by this method, and a commodity product produced from thetransgenic progeny seed of such a plant.

In another embodiment the method of this invention includes expressingin the plant at least one polynucleotide including at least 18contiguous nucleotides that are essentially identical or complementaryto a segment of equivalent length of a DNA of a target gene selectedfrom the group consisting of the genes identified in Table 1, wherebythe plant expressing the polynucleotide exhibits improved resistance toa Diabrotica species infestation, relative to an plant not expressingthe polynucleotide. In an embodiment the method includes expressing inthe plant at least one polynucleotide including at least one segment of18 or more contiguous nucleotides with a sequence of about 95% to about100% identity or complementarity with a segment of equivalent length ofa DNA of a target gene selected from the group consisting of the genesidentified in Table 1. By “expressing a polynucleotide in the plant” isgenerally meant “expressing an RNA transcript in the plant”. However,the polynucleotide expressed in the plant can also be DNA, e. g., a DNAproduced in the plant during genome replication.

The plant can be any plant that is subject to infestation by aDiabrotica species. Of particular interest are embodiments wherein theplant is a row crop plant or a vegetable crop plant. Examples include aplant selected from the group consisting of maize, cucumber, squash,soybeans, and dry beans. One row crop plant of interest is maize, andembodiments include those wherein the plant is an ungerminated maizeseed, or a maize plant in a vegetative stage (from emergence totasseling stage, i. e., VE, V1, V2, V3, . . . , V(n), VT), or a maizeplant in a reproductive stage (R1, R2, R3, R4, R5, R6). One embodimentincludes maize plants in a field of maize.

In various embodiments, the Diabrotica species is at least one selectedfrom the group consisting of Diabrotica balteata, Diabrotica barberi,Diabrotica beniensis, Diabrotica cristata, Diabrotica curvipustulata,Diabrotica dissimilis, Diabrotica elegantula, Diabrotica emorsitans,Diabrotica graminea, Diabrotica hispanolae, Diabrotica lemniscata,Diabrotica linsleyi, Diabrotica longicornis, Diabrotica milleri,Diabrotica nummularis, Diabrotica occlusa, Diabrotica porracea,Diabrotica scutellata, Diabrotica speciosa, Diabrotica tibialis,Diabrotica trifasciata, Diabrotica undecimpunctata, Diabroticavirgifera, and Diabrotica viridula. In specific embodiments, theDiabrotica species is at least one selected from the group consisting ofDiabrotica virgifera virgifera (Western Corn Rootworm, WCR), Diabroticaundecimpunctata howardii (Southern Corn Rootworm, SCR), Diabroticabarberi (Northern Corn Rootworm, NCR), Diabrotica virgifera zeae(Mexican Corn Rootworm, MCR), Diabrotica balteata (Brazilian CornRootworm, BZR), or Brazilian Corn Rootworm complex (BCR) consisting ofDiabrotica viridula and Diabrotica speciosa.

In some embodiments of the method including expressing at least onepolynucleotide in a plant, a first polynucleotide can be provided to aplant in the form of DNA (e. g., in the form of an isolated DNAmolecule, or as an expression construct, or as a transformation vector),and the polynucleotide expressed in the plant is a second polynucleotide(an RNA transcript) in the plant. In an embodiment, the polynucleotideis expressed in the plant by transgenic expression, i. e., by stablyintegrating the polynucleotide into the plant's genome from where it canbe expressed in a cell or cells of the plant. In an embodiment, a firstpolynucleotide (e. g., a recombinant DNA construct including a promoteroperably linked to DNA encoding an RNA silencing element for suppressinga target gene selected from the group consisting of the genes identifiedin Table 1) is stably integrated into the plant's genome from wheresecondarily produced polynucleotides (e. g., an RNA transcript includingthe RNA silencing element for suppressing the target gene) can beexpressed in a cell or cells of the plant. Methods of providing stablytransformed plant are provided in the section headed “Making and UsingTransgenic Plant Cells and Transgenic Plants”.

In another embodiment of this invention the polynucleotide is expressedby transient expression. In such embodiments the method can include astep of introducing a polynucleotide into the plant by routinetechniques known in the art. For example, transient expression can beaccomplished by infiltration of a polynucleotide solution using aneedle-less syringe into a leaf of a plant.

In some embodiments of this invention where the polynucleotide isexpressed by transient expression, a first polynucleotide is provided toa plant in the form of RNA or DNA or both RNA and DNA, and a secondarilyproduced second polynucleotide is transiently expressed in the plant. Inembodiments, the first polynucleotide is one or more selected from: (a)a single-stranded RNA molecule (ssRNA), (b) a single-stranded RNAmolecule that self-hybridizes to form a double-stranded RNA molecule,(c) a double-stranded RNA molecule (dsRNA), (d) a single-stranded DNAmolecule (ssDNA), (e) a single-stranded DNA molecule thatself-hybridizes to form a double-stranded DNA molecule, (f) asingle-stranded DNA molecule including a modified Pol III gene that istranscribed to an RNA molecule, (g) a double-stranded DNA molecule(dsDNA), (h) a double-stranded DNA molecule including a modified Pol IIIgene that is transcribed to an RNA molecule, and (i) a double-stranded,hybridized RNA/DNA molecule, or combinations thereof. In embodiments, afirst polynucleotide is introduced into the plant by topical applicationto the plant of a polynucleotide-containing composition in a suitableform, e. g., as a solid, liquid (including homogeneous mixtures such assolutions and non-homogeneous mixtures such as suspensions, colloids,micelles, and emulsions), powder, suspension, emulsion, spray,encapsulated or micro-encapsulation formulation, in or on microbeads orother carrier particulates, in a film or coating, or on or within amatrix. Topical application of the polynucleotide-containing compositionto the plant can be in the form of a seed treatment. Suitable binders,inert carriers, surfactants, and the like can optionally be included inthe composition, as is known to one skilled in formulation of pesticidesand seed treatments. In embodiments, the polynucleotide-containingcomposition further includes one or more components selected from thegroup consisting of a carrier agent, a surfactant, an organosilicone, apolynucleotide herbicidal molecule, a non-polynucleotide herbicidalmolecule, a non-polynucleotide pesticide, a safener, and an insectgrowth regulator. In one embodiment the composition further includes anonionic organosilicone surfactant such as Silwet, e. g., Silwet® L-77surfactant having CAS Number 27306-78-1 and EPA Number: CAL.REG.NO.5905-50073-AA, currently available from Momentive Performance Materials,Albany, N.Y. In embodiments, the topically applied composition furtherincludes at least one pesticidal agent selected from the groupconsisting of a patatin, a plant lectin, a phytoecdysteroid, a Bacillusthuringiensis insecticidal protein, a Xenorhabdus insecticidal protein,a Photorhabdus insecticidal protein, a Bacillus laterosporousinsecticidal protein, and a Bacillus sphearicus insecticidal protein.Alternatively such additional components or pesticidal agents can beprovided separately, e. g., by separate topical application or bytransgenic expression in the plant. Alternatively the plant is topicallytreated with the polynucleotide-containing composition as well as with aseparate (preceding, following, or concurrent) application of asubstance that improves the efficacy of the polynucleotide-containingcomposition. For example, a plant can be sprayed with a first topicalapplication of a solution containing a nonionic organosiliconesurfactant such as Silwet, e. g., Silwet® L-77, followed by a secondtopical application of the polynucleotide-containing composition, orvice-versa.

It is anticipated that the combination of certain polynucleotides usefulin methods of this invention (e. g., the polynucleotide triggersdescribed in the working Examples) with one or more non-polynucleotidepesticidal agents will result in a synergetic improvement in preventionor control of Diabrotica species infestations, when compared to theeffect obtained with the polynucleotide alone or the non-polynucleotidepesticidal agent alone. In an embodiment, a transgenic plant expressingone or more polynucleotides of this invention and one or more genesencoding a non-polynucleotide pesticidal agent selected from the groupconsisting of a patatin, a plant lectin, a phytoecdysteroid, a Bacillusthuringiensis insecticidal protein, a Xenorhabdus insecticidal protein,a Photorhabdus insecticidal protein, a Bacillus laterosporousinsecticidal protein, and a Bacillus sphearicus insecticidal protein, isfound to exhibit synergistically improved resistance to Diabroticaspecies infestations.

In embodiments of this invention where the polynucleotide is expressedby transient expression, a first polynucleotide is provided to a plantin the form of RNA or DNA or both RNA and DNA, and a secondarilyproduced second polynucleotide is transiently expressed in the plant;the site of application of the first polynucleotide need not be the samesite where the second polynucleotide is transiently expressed. Forexample, a first polynucleotide can be provided to a plant by topicalapplication onto a leaf, or by injection into a stem, and the secondpolynucleotide can be transiently expressed elsewhere in the plant, e.g., in the roots or throughout the plant. In some embodiments of themethod, a composition including at least one polynucleotide is topicallyapplied to above-ground parts of the plant, e. g., sprayed or dustedonto leaves, stems, and flowering parts of the plant. In otherembodiments, a composition including at least one polynucleotide istopically applied to below-ground parts of the plant, such as to theroots, e. g., by means of a soil drench. In other embodiments, acomposition including at least one polynucleotide is topically appliedto a seed that is grown into the plant having improved resistance to aDiabrotica species infestation.

The topically applied polynucleotide can be single-stranded (ss) ordouble-stranded (ds). “Double-stranded” refers to the base-pairing thatoccurs between sufficiently complementary, anti-parallel nucleic acidstrands to form a double-stranded nucleic acid structure, generallyunder physiologically relevant conditions. Embodiments of the methodinclude those wherein the polynucleotide is at least one selected fromthe group consisting of sense single-stranded DNA (ssDNA), sensesingle-stranded RNA (ssRNA), double-stranded RNA (dsRNA),double-stranded DNA (dsDNA), a double-stranded DNA/RNA hybrid,anti-sense ssDNA, or anti-sense ssRNA; a mixture of polynucleotides ofany of these types can be used.

In some embodiments of this invention a first polynucleotide (DNA or RNAor both) is topically applied to a plant and a second polynucleotidehaving a sequence corresponding to the first polynucleotide issubsequently expressed in the plant. In such embodiments thepolynucleotide expressed in the plant is an RNA transcript which can bessRNA or dsRNA or both. In various embodiments the first polynucleotideconsists of naturally occurring nucleotides, such as those which occurin DNA and RNA. In other embodiments the first polynucleotide ischemically modified, or includes chemically modified nucleotides. Thefirst polynucleotide is provided by suitable means known to one in theart. Embodiments include those wherein the first polynucleotide ischemically synthesized (e. g., by in vitro transcription, such astranscription using a T7 polymerase or other polymerase), produced byexpression in a microorganism or in cell culture (such as plant orinsect cells grown in culture), produced by expression in a plant cell,or produced by microbial fermentation. The first polynucleotide can beprovided as an RNA or DNA fragment. Alternatively the firstpolynucleotide can be provided in more complex constructs, e. g., aspart of a recombinant expression construct, or included in a recombinantvector, for example in a recombinant plant virus vector or in arecombinant baculovirus vector; such recombinant expression constructsor vectors can be designed to include additional elements, such asexpression cassettes for expressing a gene of interest (e. g., aninsecticidal protein).

In many embodiments of this invention the polynucleotide expressed inthe plant is an isolated RNA fragment and can be relatively short, suchas single- or double-stranded RNAs of between about 18 to about 200 orabout 300 nucleotides (for single-stranded RNAs) or between about 18 toabout 200 or about 300 base-pairs (for double-stranded RNAs).

The polynucleotide expressed in the plant has at least one segment of 18or more contiguous nucleotides with a sequence of about 95% to about100% identity or complementarity with a segment of equivalent length ofa DNA of a target gene selected from the group consisting of the genesidentified in Table 1. In an embodiment the polynucleotide expressed inthe plant includes at least 18 contiguous nucleotides that areessentially identical or complementary to a segment of equivalent lengthof a DNA of a target gene selected from the group consisting of thegenes identified in Table 1. In some embodiments, the contiguousnucleotides have a sequence of about 95%, about 96%, about 97%, about98%, about 99%, or about 100% identity or complementarity with thesegment of equivalent length of a DNA of a target gene selected from thegroup consisting of the genes identified in Table 1. In some embodimentsthe contiguous nucleotides are exactly (100%) identical or complementaryto a segment of equivalent length of a DNA of a target gene selectedfrom the group consisting of the genes identified in Table 1. In someembodiments, the polynucleotide has an overall sequence of about 95%,about 96%, about 97%, about 98%, about 99%, or about 100% identity orcomplementarity with a segment of a DNA of a target gene selected fromthe group consisting of the genes identified in Table 1.

The polynucleotide expressed in the plant includes at least 18contiguous nucleotides with a sequence of about 95% to about 100%identity or complementarity with a segment of equivalent length of a DNAof a target gene selected from the group consisting of the genesidentified in Table 1. The contiguous nucleotides number at least 18, e.g., between 18-24, or between 18-28, or between 20-30, or between 20-50,or between 20-100, or between 50-100, or between 100-250, or between100-500, or between 200-1000, or between 500-2000, or even greater, forexample, up to the entire length of an open reading frame or up to theentire length of a gene or nucleotide sequence to be suppressed. Thecontiguous nucleotides can number more than 18, e. g., 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, or greater than 30, e. g., about 35,about 40, about 45, about 50, about 55, about 60, about 65, about 70,about 75, about 80, about 85, about 90, about 95, about 100, about 110,about 120, about 130, about 140, about 150, about 160, about 170, about180, about 190, about 200, about 210, about 220, about 230, about 240,about 250, about 260, about 270, about 280, about 290, about 300, orgreater than 300.

The polynucleotide expressed in the plant is generally designed tosuppress one or more genes (“target genes”). Such target genes caninclude coding or non-coding sequence or both. In specific embodiments,the polynucleotide expressed in the plant is designed to suppress one ormore target genes, where at least one target gene is selected from thegroup consisting of the genes identified in Table 1. In variousembodiments, the polynucleotide expressed in the plant is designed tosuppress one or more genes, where each target gene is selected from thegroup consisting of the genes identified in Table 1, and can be designedto suppress multiple genes from this group, or to target differentregions of one or more of these genes. In an embodiment, thepolynucleotide expressed in the plant includes multiple sections orsegments each of which includes at least 18 contiguous nucleotides witha sequence of about 95% to about 100% identity or complementarity with asegment of equivalent length of a DNA of a target gene selected from thegroup consisting of the genes identified in Table 1. In such cases, eachsection can be identical or different in size or in sequence, and can besense or anti-sense relative to the target gene. For example, in oneembodiment the polynucleotide expressed in the plant can includemultiple sections in tandem or repetitive arrangements, wherein eachsection includes at least 18 contiguous nucleotides with a sequence ofabout 95% to about 100% identity or complementarity with a segment ofequivalent length of a DNA of a target gene selected from the groupconsisting of the genes identified in Table 1; “spacer” nucleotideswhich do not correspond to a target gene can optionally be used inbetween the sections.

The total length of the polynucleotide expressed in the plant can begreater than 18 contiguous nucleotides, and can include nucleotides inaddition to the contiguous nucleotides having the sequence of about 95%to about 100% identity or complementarity with a segment of equivalentlength of a DNA of a target gene selected from the group consisting ofthe genes identified in Table 1. In other words, the total length of thepolynucleotide expressed in the plant can be greater than the length ofthe section or segment of the polynucleotide designed to suppress one ormore target genes, where each target gene is selected from the groupconsisting of the genes identified in Table 1. For example, thepolynucleotide expressed in the plant can have nucleotides flanking the“active” segment of at least 18 contiguous nucleotides that suppressesthe target gene, or include “spacer” nucleotides between activesegments, or can have additional nucleotides at the 5′ end, or at the 3′end, or at both the 5′ and 3′ ends. In an embodiment, the polynucleotideexpressed in the plant can include additional nucleotides that providestabilizing secondary structure.

In a related aspect, this invention is directed to the plant havingimproved resistance to a Diabrotica species infestation, provided byexpressing in the plant at least one polynucleotide including at least18 contiguous nucleotides that are essentially identical orcomplementary to a segment of equivalent length of a DNA of a targetgene selected from the group consisting of the genes identified in Table1, whereby the resulting plant has improved resistance to a Diabroticaspecies infestation when compared to a control plant in which thepolynucleotide is not expressed. In a related aspect, this invention isdirected to the plant having improved resistance to a Diabrotica speciesinfestation, provided by expressing in the plant at least onepolynucleotide including at least one segment of 18 or more contiguousnucleotides with a sequence of about 95% to about 100% identity orcomplementarity with a segment of equivalent length of a DNA of a targetgene selected from the group consisting of the genes identified in Table1, whereby the resulting plant has improved resistance to a Diabroticaspecies infestation when compared to a control plant in which thepolynucleotide is not expressed. In yet another aspect, this inventionis directed to seed (especially transgenic progeny seed) produced by theplant having improved resistance to a Diabrotica species infestation, asprovided by this method. Also contemplated is a commodity productproduced by the plant having improved resistance to a Diabrotica speciesinfestation, as provided by this method, and a commodity productproduced from the transgenic progeny seed of such a plant.

Methods of Controlling Diabrotica Species Infestations of a Plant

Another aspect of this invention provides a method for controlling aDiabrotica species infestation of a plant including contacting theDiabrotica species with a polynucleotide including at least 18contiguous nucleotides that are essentially identical or complementaryto a segment of equivalent length of a target gene selected from thegroup consisting of the genes identified in Table 1. Embodiments ofthese target genes are identified by name in Table 1 and include geneshaving a sequence selected from the group consisting of SEQ IDNOs:1-450, as well as related genes including orthologues from relatedinsect species, for example, related genes from other Diabroticaspecies, Tribolium species, or other related coleopteran genera.Examples of such related genes include the Tribolium castaneum geneslisted in Table 1. In this context “controlling” includes inducement ofa physiological or behavioural change such as, but not limited to,growth stunting, increased mortality, decrease in reproductive capacity,decrease in or cessation of feeding behavior or movement, or decrease inor cessation of metamorphosis stage development.

In various embodiments, the Diabrotica species is at least one selectedfrom the group consisting of Diabrotica balteata, Diabrotica barberi,Diabrotica beniensis, Diabrotica cristata, Diabrotica curvipustulata,Diabrotica dissimilis, Diabrotica elegantula, Diabrotica emorsitans,Diabrotica graminea, Diabrotica hispanolae, Diabrotica lemniscata,Diabrotica linsleyi, Diabrotica longicornis, Diabrotica milleri,Diabrotica nummularis, Diabrotica occlusa, Diabrotica porracea,Diabrotica scutellata, Diabrotica speciosa, Diabrotica tibialis,Diabrotica trifasciata, Diabrotica undecimpunctata, Diabroticavirgifera, and Diabrotica viridula. In specific embodiments, theDiabrotica species is at least one selected from the group consisting ofDiabrotica virgifera virgifera (Western Corn Rootworm, WCR), Diabroticaundecimpunctata howardii (Southern Corn Rootworm, SCR), Diabroticabarberi (Northern Corn Rootworm, NCR), Diabrotica virgifera zeae(Mexican Corn Rootworm, MCR), Diabrotica balteata (Brazilian CornRootworm, BZR), or Brazilian Corn Rootworm complex (BCR) consisting ofDiabrotica viridula and Diabrotica speciosa.

The plant can be any plant that is subject to infestation by aDiabrotica species. Of particular interest are embodiments wherein theplant is a row crop plant or a vegetable crop plant. Examples include aplant selected from the group consisting of maize, cucumber, squash,soybeans, and dry beans. One row crop plant of interest is maize, andembodiments include those wherein the plant is an ungerminated maizeseed, or a maize plant in a vegetative stage (from emergence totasseling stage, i. e., VE, V1, V2, V3, . . . , V(n), VT), or a maizeplant in a reproductive stage (R1, R2, R3, R4, R5, R6). One embodimentincludes maize plants in a field of maize.

The polynucleotide of use in methods of this invention can besingle-stranded (ss) or double-stranded (ds). “Double-stranded” refersto the base-pairing that occurs between sufficiently complementary,anti-parallel nucleic acid strands to form a double-stranded nucleicacid structure, generally under physiologically relevant conditions.Embodiments of the method include those wherein the polynucleotide is atleast one selected from the group consisting of sense single-strandedDNA (ssDNA), sense single-stranded RNA (ssRNA), double-stranded RNA(dsRNA), double-stranded DNA (dsDNA), a double-stranded DNA/RNA hybrid,anti-sense ssDNA, or anti-sense ssRNA; a mixture of polynucleotides ofany of these types can be used.

The polynucleotide of use in methods of this invention includes at least18 contiguous nucleotides that are essentially identical orcomplementary to a segment of equivalent length of a target geneselected from the group consisting of the genes identified in Table 1.In some embodiments, the contiguous nucleotides have a sequence of about95%, about 96%, about 97%, about 98%, about 99%, or about 100% identityor complementarity with the segment of equivalent length of a targetgene selected from the group consisting of the genes identified inTable 1. In some embodiments the contiguous nucleotides are exactly(100%) identical or complementary to a segment of equivalent length of atarget gene selected from the group consisting of the genes identifiedin Table 1. In some embodiments, the polynucleotide has an overallsequence of about 95%, about 96%, about 97%, about 98%, about 99%, orabout 100% identity or complementarity with a segment of equivalentlength of a target gene selected from the group consisting of the genesidentified in Table 1.

Polynucleotides of use in methods of this invention include at least 18contiguous nucleotides with a sequence of about 95% to about 100%identity or complementarity with a segment of equivalent length of atarget gene selected from the group consisting of the genes identifiedin Table 1. The contiguous nucleotides number at least 18, e. g.,between 18-24, or between 18-28, or between 20-30, or between 20-50, orbetween 20-100, or between 50-100, or between 100-250, or between100-500, or between 200-1000, or between 500-2000, or even greater, forexample, up to the entire length of an open reading frame or up to theentire length of a gene or nucleotide sequence to be suppressed. Thecontiguous nucleotides can number more than 18, e. g., 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, or greater than 30, e. g., about 35,about 40, about 45, about 50, about 55, about 60, about 65, about 70,about 75, about 80, about 85, about 90, about 95, about 100, about 110,about 120, about 130, about 140, about 150, about 160, about 170, about180, about 190, about 200, about 210, about 220, about 230, about 240,about 250, about 260, about 270, about 280, about 290, about 300, orgreater than 300.

The polynucleotide of use in methods of this invention is generallydesigned to suppress one or more genes (“target genes”). The term “gene”refers to any portion of a nucleic acid that provides for expression ofa transcript or encodes a transcript. A “gene” thus includes, but is notlimited to, a promoter region, 5′ untranslated regions, transcriptencoding regions that can include intronic regions, and 3′ untranslatedregions. Thus, the target genes can include coding or non-codingsequence or both. In specific embodiments, the polynucleotide isdesigned to suppress one or more target genes, where at least one targetgene is selected from the group consisting of the genes identified inTable 1. In various embodiments, the polynucleotide is designed tosuppress one or more genes, where each gene is selected from the groupconsisting of the genes identified in Table 1, and can be designed tosuppress multiple genes from this group, or to target different regionsof one or more of these genes. In an embodiment, the polynucleotideincludes multiple sections or segments each of which includes at least18 contiguous nucleotides with a sequence of about 95% to about 100%identity or complementarity with a segment of equivalent length of atarget gene selected from the group consisting of the genes identifiedin Table 1. In such cases, each section can be identical or different insize or in sequence, and can be sense or anti-sense relative to thetarget gene. For example, in one embodiment the polynucleotide caninclude multiple sections in tandem or repetitive arrangements, whereineach section includes at least 18 contiguous nucleotides with a sequenceof about 95% to about 100% identity or complementarity with a segment ofequivalent length of a target gene selected from the group consisting ofthe genes identified in Table 1; “spacer” nucleotides which do notcorrespond to a target gene can optionally be used in between thesections.

The total length of the polynucleotide of use in methods of thisinvention can be greater than 18 contiguous nucleotides, and can includenucleotides in addition to the contiguous nucleotides having thesequence of about 95% to about 100% identity or complementarity with asegment of equivalent length of a target gene selected from the groupconsisting of the genes identified in Table 1. In other words, the totallength of the polynucleotide can be greater than the length of thesection or segment of the polynucleotide designed to suppress one ormore target genes, where each target gene is selected from the groupconsisting of the genes identified in Table 1. For example, thepolynucleotide can have nucleotides flanking the “active” segment of atleast 18 contiguous nucleotides that suppresses the target gene, orinclude “spacer” nucleotides between active segments, or can haveadditional nucleotides at the 5′ end, or at the 3′ end, or at both the5′ and 3′ ends. In an embodiment, the polynucleotide can includeadditional nucleotides that provide stabilizing secondary structure.

In various embodiments the polynucleotide of use in methods of thisinvention consists of naturally occurring nucleotides, such as thosewhich occur in DNA and RNA. In certain embodiments, the polynucleotideis a combination of ribonucleotides and deoxyribonucleotides, forexample, synthetic polynucleotides consisting mainly of ribonucleotidesbut with one or more terminal deoxyribonucleotides or syntheticpolynucleotides consisting mainly of deoxyribonucleotides but with oneor more terminal dideoxyribonucleotides. In certain embodiments, thepolynucleotide includes non-canonical nucleotides such as inosine,thiouridine, or pseudouridine. In certain embodiments, thepolynucleotide includes chemically modified nucleotides. Examples ofchemically modified oligonucleotides or polynucleotides are well knownin the art; see, for example, U.S. Patent Publication 2011/0171287, U.S.Patent Publication 2011/0171176, U.S. Patent Publication 2011/0152353,U.S. Patent Publication 2011/0152346, and U.S. Patent Publication2011/0160082, which are herein incorporated by reference. Illustrativeexamples include, but are not limited to, the naturally occurringphosphodiester backbone of an oligonucleotide or polynucleotide whichcan be partially or completely modified with phosphorothioate,phosphorodithioate, or methylphosphonate internucleotide linkagemodifications, modified nucleoside bases or modified sugars can be usedin oligonucleotide or polynucleotide synthesis, and oligonucleotides orpolynucleotides can be labeled with a fluorescent moiety (e. g.,fluorescein or rhodamine) or other label (e. g., biotin).

The polynucleotide of use in methods of this invention is provided bysuitable means known to one in the art. Embodiments include thosewherein the polynucleotide is chemically synthesized (e. g., by in vitrotranscription, such as transcription using a T7 polymerase or otherpolymerase), produced by expression in a microorganism or in cellculture (such as plant or insect cells grown in culture), produced byexpression in a plant cell, or produced by microbial fermentation.

In many embodiments the polynucleotide of use in methods of thisinvention is provided as an isolated DNA or RNA fragment (not part of anexpression construct, i. e., lacking additional elements such as apromoter or terminator sequences). Such polynucleotides can berelatively short, such as single- or double-stranded polynucleotides ofbetween about 18 to about 200 or about 300 nucleotides (forsingle-stranded polynucleotides) or between about 18 to about 200 orabout 300 base-pairs (for double-stranded polynucleotides).Alternatively the polynucleotide can be provided in more complexconstructs, e. g., as part of a recombinant expression construct, orincluded in a recombinant vector, for example in a recombinant plantvirus vector or in a recombinant baculovirus vector. Such recombinantexpression constructs or vectors can be designed to include additionalelements, such as expression cassettes for expressing a gene of interest(e. g., an insecticidal protein).

In various embodiments of the method, the contacting includesapplication to a surface of the Diabrotica species of a suitablecomposition including the polynucleotide; such a composition can beprovided, e. g., as a solid, liquid (including homogeneous mixtures suchas solutions and non-homogeneous mixtures such as suspensions, colloids,micelles, and emulsions), powder, suspension, emulsion, spray,encapsulated or micro-encapsulation formulation, in or on microbeads orother carrier particulates, in a film or coating, or on or within amatrix. The contacting can be in the form of a seed treatment. Suitablebinders, inert carriers, surfactants, and the like can optionally beincluded in the composition, as is known to one skilled in formulationof pesticides and seed treatments. In embodiments, the contactingincludes providing the polynucleotide in a composition that furtherincludes one or more components selected from the group consisting of acarrier agent, a surfactant, an organosilicone, a polynucleotideherbicidal molecule, a non-polynucleotide herbicidal molecule, anon-polynucleotide pesticide, a safener, and an insect growth regulator.In embodiments, the contacting includes providing the polynucleotide ina composition that further includes at least one pesticidal agentselected from the group consisting of a patatin, a plant lectin, aphytoecdysteroid, a Bacillus thuringiensis insecticidal protein, aXenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, aBacillus laterosporous insecticidal protein, and a Bacillus sphearicusinsecticidal protein. In one embodiment the contacting includesproviding the polynucleotide in a composition that can be ingested orotherwise absorbed internally by the Diabrotica species.

Methods of Selecting Target Genes

Another aspect of this invention provides a method of selectingpreferred target genes for RNAi-mediated silencing. In an embodiment,the method provides a subset of target genes that are present in single-or low-copy-number (i. e., non-repetitive and non-redundant) in aparticular genome. Such preferred target genes can be genes from a plantgenome or genes from an animal genome. In embodiments, the preferredtarget genes are genes of an invertebrate pest, e. g. an invertebratepest of a plant or an invertebrate pest of a vertebrate. In embodiments,the preferred target genes are genes of an insect pest of a plant or anematode pest of a plant. In embodiments, the preferred target genes aregenes of a Diabrotica species. Further aspects of this invention includemanufacturing a polynucleotide of this invention (e. g., an ssRNA ordsRNA trigger, such as the dsRNA triggers described in the workingExamples, or a recombinant DNA construct of this invention useful formaking transgenic plants) based on preferred target genes forRNAi-mediated silencing selected by any of the methods described herein.

In an embodiment, the method includes the step of identifying single- orlow-copy-number genes in the chosen genome, or alternatively to identifysingle- or low-copy-number genes in an orthologous database from relatedorganisms to predict which genes will be single/low copy in the chosenorganism. Low-copy genes, and in particular single-copy genes, areselected as preferred targets for RNAi-mediated silencing. In oneembodiment, the identification of single- or low-copy-number genes iscarried out by sequence comparison between a set of genes from a firstspecies and a set of genes from a second species, wherein the set ofgenes from a second species have been identified as single- orlow-copy-number in the second species. In one embodiment, theidentification of single- or low-copy-number genes is carried out byapplying an algorithm performed by a computer to a set of genes from afirst species to identify a subset of single- or low-copy-number genesin the set of genes from the first species, then comparing a set ofgenes from a second species to the subset of single- or low-copy-numbergenes from the first species to identify corresponding single- orlow-copy-number genes from the second species. The single- orlow-copy-number genes from the second species are useful as preferredtarget genes for RNAi-mediated silencing; the sequences of thesepreferred target genes are used for designing polynucleotides (e. g., anssRNA or dsRNA trigger, such as the dsRNA triggers described in theworking Examples, or recombinant DNA constructs for making transgenicplants) and methods of use thereof for preventing or controllinginfestations by the second species.

Embodiments of the method include a further step of estimatingnucleotide diversity for low-/single-copy genes in a population of thechosen organism and selecting those low-/single-copy genes that furtherhave the lowest nucleotide diversity. Low-/single-copy genes thatfurther have low nucleotide diversity are selected as preferred targetsfor RNAi-mediated silencing.

Embodiments of the method include a further step of comparing the ratioof synonymous (K_(s)) to nonsynonymous (K_(a)) nucleotide changes as anestimate of functional or evolutionary constraint. In an embodiment, themethod includes the step of selecting genes where K_(s) is at leastequal to or greater than K_(a). In an embodiment, the method includesthe step of selecting genes where K_(s)>>K_(a).

A related aspect of this invention is a set of preferred target genesfor RNAi-mediated silencing identified from a genome by any of the geneselection methods described herein. An embodiment includes a set ofpreferred target genes for RNAi-mediated silencing selected from agenome by identifying single- or low-copy-number target genes from alarger set of genes from that genome. One embodiment includes a set ofpreferred target genes for RNAi-mediated silencing selected from aninvertebrate genome by identifying single- or low-copy-number targetgenes from a larger set of genes from that invertebrate genome. Aspecific embodiment includes a set of preferred target genes forRNAi-mediated silencing in a Diabrotica species selected from aDiabrotica genome by identifying single- or low-copy-number target genesfrom a larger set of genes from that Diabrotica genome.

Another embodiment includes a set of preferred target genes forRNAi-mediated silencing selected from a genome by estimating nucleotidediversity for a given set of genes in a population of individuals of thespecies having that genome, and selecting those genes that have thelowest nucleotide diversity. One embodiment includes a set of preferredtarget genes for RNAi-mediated silencing selected from an invertebrategenome by estimating nucleotide diversity for a given set of genes in apopulation of individuals of the invertebrate having that genome, andselecting those genes that have the lowest nucleotide diversity. Anotherembodiment includes a set of preferred target genes for RNAi-mediatedsilencing selected from an invertebrate genome by estimating nucleotidediversity for low-/single-copy genes in a population of individuals ofthe invertebrate having that genome, and selecting thoselow-/single-copy genes that further have the lowest nucleotidediversity.

Another embodiment includes a set of preferred target genes forRNAi-mediated silencing selected from a genome by comparing the ratio ofsynonymous (K_(s)) to nonsynonymous (K_(a)) nucleotide changes in genesof that genome and selecting genes where K_(s) is at least equal to orgreater than K_(a). In an embodiment, the set of preferred target genesfor RNAi-mediated silencing are genes where K_(s) is at least equal toor greater than K_(a). In an embodiment, the set of preferred targetgenes for RNAi-mediated silencing are genes where K_(s)>>K_(a). Anembodiment includes a set of preferred target genes for RNAi-mediatedsilencing selected from an invertebrate genome and where K_(s)>>K_(a)for the selected genes.

In an embodiment, the single- or low-copy-number target genes are asubset of target genes of a first invertebrate species selected from alarger set of genes from the first invertebrate species, wherein theselection is by a sequence comparison performed by a computer betweenthe larger set of genes from the first invertebrate species and a set ofgenes from a second invertebrate species that have been identified assingle- or low-copy-number in the second invertebrate species. In aspecific embodiment, the single- or low-copy-number target genes are asubset of Diabrotica virgifera virgifera target genes selected from alarger set of Diabrotica virgifera virgifera target genes, wherein theselection is by a sequence comparison performed by a computer betweenthe larger set of Diabrotica virgifera virgifera target genes and a setof genes from a second invertebrate species that have been identified assingle- or low-copy-number in the second invertebrate species. Thepreferred Diabrotica virgifera virgifera single- or low-copy-numbertarget genes selected by the method are particularly useful in makingpolynucleotides of this invention, including recombinant DNA constructsuseful, e. g., for providing plants having increased resistance to aDiabrotica species infestation, and isolated recombinant RNA moleculesuseful, e. g., in making compositions for topical treatment of a plantor Diabrotica species to provide prevention or control of a Diabroticaspecies infestations. In an embodiment, preferred Diabrotica virgiferavirgifera single- or low-copy-number target genes selected by the methodare genes having a sequence selected from the group consisting of SEQ IDNOs:1-450.

A further aspect of this invention are polyclonal or monoclonalantibodies that bind a protein encoded by a sequence or a fragment of asequence selected from the group consisting of SEQ ID NOs:1-450; suchantibodies are made by routine methods as known to one of ordinary skillin the art, for example using routine protocols as described in“Antibody Methods and Protocols” (Proetzel and Ebersbach, editors, 2012,Humana Press, New York) or “Making and Using Antibodies” (Howard andKaser, editors, 2006, CRC Press, Boca Raton).

Related Techniques

Embodiments of the polynucleotides and nucleic acid molecules of thisinvention can include additional elements, such as promoters, small RNArecognition sites, aptamers or ribozymes, additional and additionalexpression cassettes for expressing coding sequences (e. g., to expressa transgene such as an insecticidal protein or selectable marker) ornon-coding sequences (e. g., to express additional suppressionelements). For example, an aspect of this invention provides arecombinant DNA construct including a heterologous promoter operablylinked to DNA including at least one segment of 18 or more contiguousnucleotides with a sequence of about 95% to about 100% identity with asegment of equivalent length of a DNA having a sequence selected fromthe group consisting of SEQ ID NOs:1-450 or the DNA complement thereof.In another embodiment, a recombinant DNA construct including a promoteroperably linked to DNA encoding: (a) an RNA silencing element forsuppressing a target gene selected from the group consisting of thegenes identified in Table 1), and (b) an aptamer, is stably integratedinto the plant's genome from where RNA transcripts including the RNAaptamer and the RNA silencing element are expressed in cells of theplant; the aptamer serves to guide the RNA silencing element to adesired location in the cell. In another embodiment, inclusion of one ormore recognition sites for binding and cleavage by a small RNA (e. g.,by a miRNA or an siRNA that is expressed only in a particular cell ortissue) allows for more precise expression patterns in a plant, whereinthe expression of the recombinant DNA construct is suppressed where thesmall RNA is expressed. Such additional elements are described below.

Promoters

Promoters of use in the invention are functional in the cell in whichthe construct is intended to be transcribed. Generally these promotersare heterologous promoters, as used in recombinant constructs, i. e.,they are not in nature found to be operably linked to the other nucleicelements used in the constructs of this invention. In variousembodiments, the promoter is selected from the group consisting of aconstitutive promoter, a spatially specific promoter, a temporallyspecific promoter, a developmentally specific promoter, and an induciblepromoter. In many embodiments the promoter is a promoter functional in aplant, for example, a pol II promoter, a pol III promoter, a pol IVpromoter, or a pol V promoter.

Non-constitutive promoters suitable for use with the recombinant DNAconstructs of this invention include spatially specific promoters,temporally specific promoters, and inducible promoters. Spatiallyspecific promoters can include organelle-, cell-, tissue-, ororgan-specific promoters (e. g., a plastid-specific, a root-specific, apollen-specific, or a seed-specific promoter for expression in plastids,roots, pollen, or seeds, respectively). In many cases a seed-specific,embryo-specific, aleurone-specific, or endosperm-specific promoter isespecially useful. Temporally specific promoters can include promotersthat tend to promote expression during certain developmental stages in aplant's growth cycle, or during different times of day or night, or atdifferent seasons in a year. Inducible promoters include promotersinduced by chemicals or by environmental conditions such as, but notlimited to, biotic or abiotic stress (e. g., water deficit or drought,heat, cold, high or low nutrient or salt levels, high or low lightlevels, or pest or pathogen infection). MicroRNA promoters are useful,especially those having a temporally specific, spatially specific, orinducible expression pattern; examples of miRNA promoters, as well asmethods for identifying miRNA promoters having specific expressionpatterns, are provided in U.S. Patent Application Publications2006/0200878, 2007/0199095, and 2007/0300329, which are specificallyincorporated herein by reference. An expression-specific promoter canalso include promoters that are generally constitutively expressed butat differing degrees or “strengths” of expression, including promoterscommonly regarded as “strong promoters” or as “weak promoters”.

Promoters of particular interest include the following examples: anopaline synthase promoter isolated from T-DNA of Agrobacterium; acauliflower mosaic virus 35S promoter; enhanced promoter elements orchimeric promoter elements such as an enhanced cauliflower mosaic virus(CaMV) 35S promoter linked to an enhancer element (an intron from heatshock protein 70 of Zea mays); root specific promoters such as thosedisclosed in U.S. Pat. Nos. 5,837,848; 6,437,217 and 6,426,446; a maizeL3 oleosin promoter disclosed in U.S. Pat. No. 6,433,252; a promoter fora plant nuclear gene encoding a plastid-localized aldolase disclosed inU.S. Patent Application Publication 2004/0216189; cold-induciblepromoters disclosed in U.S. Pat. No. 6,084,089; salt-inducible promotersdisclosed in U.S. Pat. No. 6,140,078; light-inducible promotersdisclosed in U.S. Pat. No. 6,294,714; pathogen-inducible promotersdisclosed in U.S. Pat. No. 6,252,138; and water deficit-induciblepromoters disclosed in U.S. Patent Application Publication 2004/0123347A1. All of the above-described patents and patent publicationsdisclosing promoters and their use, especially in recombinant DNAconstructs functional in plants are incorporated herein by reference.

Plant vascular- or phloem-specific promoters of interest include a rolCor rolA promoter of Agrobacterium rhizogenes, a promoter of aAgrobacterium tumefaciens T-DNA gene 5, the rice sucrose synthase RSs1gene promoter, a Commelina yellow mottle badnavirus promoter, a coconutfoliar decay virus promoter, a rice tungro bacilliform virus promoter,the promoter of a pea glutamine synthase GS3A gene, a invCD111 andinvCD141 promoters of a potato invertase genes, a promoter isolated fromArabidopsis shown to have phloem-specific expression in tobacco byKertbundit et al. (1991) Proc. Natl. Acad. Sci. USA., 88:5212-5216, aVAHOX1 promoter region, a pea cell wall invertase gene promoter, an acidinvertase gene promoter from carrot, a promoter of a sulfate transportergene Sultr1;3, a promoter of a plant sucrose synthase gene, and apromoter of a plant sucrose transporter gene.

Promoters suitable for use with a recombinant DNA construct orpolynucleotide of this invention include polymerase II (“pol II”)promoters and polymerase III (“pol III”) promoters. RNA polymerase IItranscribes structural or catalytic RNAs that are usually shorter than400 nucleotides in length, and recognizes a simple run of T residues asa termination signal; it has been used to transcribe siRNA duplexes(see, e. g., Lu et al. (2004) Nucleic Acids Res., 32:e171). Pol IIpromoters are therefore preferred in certain embodiments where a shortRNA transcript is to be produced from a recombinant DNA construct ofthis invention. In one embodiment, the recombinant DNA constructincludes a pol II promoter to express an RNA transcript flanked byself-cleaving ribozyme sequences (e. g., self-cleaving hammerheadribozymes), resulting in a processed RNA, such as a single-stranded RNAthat binds to the transcript of the Diabrotica target gene, with defined5′ and 3′ ends, free of potentially interfering flanking sequences. Analternative approach uses pol III promoters to generate transcripts withrelatively defined 5′ and 3′ ends, i. e., to transcribe an RNA withminimal 5′ and 3′ flanking sequences. In some embodiments, Pol IIIpromoters (e. g., U6 or H1 promoters) are preferred for adding a shortAT-rich transcription termination site that results in 2 base-pairoverhangs (UU) in the transcribed RNA; this is useful, e. g., forexpression of siRNA-type constructs. Use of pol III promoters fordriving expression of siRNA constructs has been reported; see van deWetering et al. (2003) EMBO Rep., 4: 609-615, and Tuschl (2002) NatureBiotechnol., 20: 446-448.

The promoter element can include nucleic acid sequences that are notnaturally occurring promoters or promoter elements or homologues thereofbut that can regulate expression of a gene. Examples of such “geneindependent” regulatory sequences include naturally occurring orartificially designed RNA sequences that include a ligand-binding regionor aptamer (see “Aptamers”, below) and a regulatory region (which can becis-acting). See, for example, Isaacs et al. (2004) Nat. Biotechnol.,22:841-847, Bayer and Smolke (2005) Nature Biotechnol., 23:337-343,Mandal and Breaker (2004) Nature Rev. Mol. Cell Biol., 5:451-463,Davidson and Ellington (2005) Trends Biotechnol., 23:109-112, Winkler etal. (2002) Nature, 419:952-956, Sudarsan et al. (2003) RNA, 9:644-647,and Mandal and Breaker (2004) Nature Struct. Mol. Biol., 11:29-35. Such“riboregulators” could be selected or designed for specific spatial ortemporal specificity, for example, to regulate translation of DNA thatencodes a silencing element for suppressing a Diabrotica target geneonly in the presence (or absence) of a given concentration of theappropriate ligand. One example is a riboregulator that is responsive toan endogenous ligand (e. g., jasmonic acid or salicylic acid) producedby the plant when under stress (e. g., abiotic stress such as water,temperature, or nutrient stress, or biotic stress such as attach bypests or pathogens); under stress, the level of endogenous ligandincreases to a level sufficient for the riboregulator to begintranscription of the DNA that encodes a silencing element forsuppressing a Diabrotica target gene.

Recombinase Sites

In some embodiments, the recombinant DNA construct or polynucleotide ofthis invention includes DNA encoding one or more site-specificrecombinase recognition sites. In one embodiment, the recombinant DNAconstruct includes at least a pair of loxP sites, wherein site-specificrecombination of DNA between the loxP sites is mediated by a Crerecombinase. The position and relative orientation of the loxP sites isselected to achieve the desired recombination; for example, when theloxP sites are in the same orientation, the DNA between the loxP sitesis excised in circular form. In another embodiment, the recombinant DNAconstruct includes DNA encoding one loxP site; in the presence of Crerecombinase and another DNA with a loxP site, the two DNAs arerecombined.

Aptamers

In some embodiments, the recombinant DNA construct or polynucleotide ofthis invention includes DNA that is processed to an RNA aptamer, thatis, an RNA that binds to a ligand through binding mechanism that is notprimarily based on Watson-Crick base-pairing (in contrast, for example,to the base-pairing that occurs between complementary, anti-parallelnucleic acid strands to form a double-stranded nucleic acid structure).See, for example, Ellington and Szostak (1990) Nature, 346:818-822.Examples of aptamers can be found, for example, in the public AptamerDatabase, available on line at aptamer.icmb.utexas.edu (Lee et al.(2004) Nucleic Acids Res., 32(1):D95-100). Aptamers useful in theinvention can, however, be monovalent (binding a single ligand) ormultivalent (binding more than one individual ligand, e. g., binding oneunit of two or more different ligands).

Ligands useful in the invention include any molecule (or part of amolecule) that can be recognized and be bound by a nucleic acidsecondary structure by a mechanism not primarily based on Watson-Crickbase pairing. In this way, the recognition and binding of ligand andaptamer is analogous to that of antigen and antibody, or of biologicaleffector and receptor. Ligands can include single molecules (or part ofa molecule), or a combination of two or more molecules (or parts of amolecule), and can include one or more macromolecular complexes (e. g.,polymers, lipid bilayers, liposomes, cellular membranes or othercellular structures, or cell surfaces). Examples of specific ligandsinclude vitamins such as coenzyme B₁₂ and thiamine pyrophosphate, flavinmononucleotide, guanine, adenosine, S-adenosylmethionine,S-adenosylhomocysteine, coenzyme A, lysine, tyrosine, dopamine,glucosamine-6-phosphate, caffeine, theophylline, antibiotics such aschloramphenicol and neomycin, herbicides such as glyphosate and dicamba,proteins including viral or phage coat proteins and invertebrateepidermal or digestive tract surface proteins, and RNAs including viralRNA, transfer-RNAs (t-RNAs), ribosomal RNA (rRNA), and RNA polymerasessuch as RNA-dependent RNA polymerase (RdRP). One class of RNA aptamersuseful in the invention are “thermoswitches” that do not bind a ligandbut are thermally responsive, that is to say, the aptamer's conformationis determined by temperature; see, for example, Box 3 in Mandal andBreaker (2004) Nature Rev. Mol. Cell Biol., 5:451-463.

Transgene Transcription Units

In some embodiments, the recombinant DNA construct or polynucleotide ofthis invention includes a transgene transcription unit. A transgenetranscription unit includes DNA sequence encoding a gene of interest, e.g., a natural protein or a heterologous protein. A gene of interest canbe any coding or non-coding sequence from any species (including, butnot limited to, non-eukaryotes such as bacteria, and viruses; fungi,protists, plants, invertebrates, and vertebrates. Particular genes ofinterest are genes encoding at least one pesticidal agent selected fromthe group consisting of a patatin, a plant lectin, a phytoecdysteroid, aphytoecdysteroid, a Bacillus thuringiensis insecticidal protein, aXenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, aBacillus laterosporous insecticidal protein, and a Bacillus sphearicusinsecticidal protein. The transgene transcription unit can furtherinclude 5′ or 3′ sequence or both as required for transcription of thetransgene.

Introns

In some embodiments, the recombinant DNA construct or polynucleotide ofthis invention includes DNA encoding a spliceable intron. By “intron” isgenerally meant a segment of DNA (or the RNA transcribed from such asegment) that is located between exons (protein-encoding segments of theDNA or corresponding transcribed RNA), wherein, during maturation of themessenger RNA, the intron present is enzymatically “spliced out” orremoved from the RNA strand by a cleavage/ligation process that occursin the nucleus in eukaryotes. The term “intron” is also applied tonon-coding DNA sequences that are transcribed to RNA segments that canbe spliced out of a maturing RNA transcript, but are not introns foundbetween protein-coding exons. One example of these are spliceablesequences that that have the ability to enhance expression in plants (insome cases, especially in monocots) of a downstream coding sequence;these spliceable sequences are naturally located in the 5′ untranslatedregion of some plant genes, as well as in some viral genes (e. g., thetobacco mosaic virus 5′ leader sequence or “omega” leader described asenhancing expression in plant genes by Gallie and Walbot (1992) NucleicAcids Res., 20:4631-4638). These spliceable sequences or“expression-enhancing introns” can be artificially inserted in the 5′untranslated region of a plant gene between the promoter but before anyprotein-coding exons. Examples of such expression-enhancing intronsinclude, but are not limited to, a maize alcohol dehydrogenase(Zm-Adh1), a maize Bronze-1 expression-enhancing intron, a rice actin 1(Os-Act1) intron, a Shrunken-1 (Sh-1) intron, a maize sucrose synthaseintron, a heat shock protein 18 (hsp18) intron, and an 82 kilodaltonheat shock protein (hsp82) intron. U.S. Pat. Nos. 5,593,874 and5,859,347, specifically incorporated by reference herein, describemethods of improving recombinant DNA constructs for use in plants byinclusion of an expression-enhancing intron derived from the 70kilodalton maize heat shock protein (hsp70) in the non-translated leaderpositioned 3′ from the gene promoter and 5′ from the firstprotein-coding exon.

Ribozymes

In some embodiments, the recombinant DNA construct or polynucleotide ofthis invention includes DNA encoding one or more ribozymes. Ribozymes ofparticular interest include a self-cleaving ribozyme, a hammerheadribozyme, or a hairpin ribozyme. In one embodiment, the recombinant DNAconstruct includes DNA encoding one or more ribozymes that serve tocleave the transcribed RNA to provide defined segments of RNA, such assilencing elements for suppressing a Diabrotica target gene.

Gene Suppression Elements

In some embodiments, the recombinant DNA construct or polynucleotide ofthis invention includes DNA encoding an additional gene suppressionelement for suppressing a target gene other than a Diabrotica targetgene. The target gene to be suppressed can include coding or non-codingsequence or both.

Suitable gene suppression elements are described in detail in U.S.Patent Application Publication 2006/0200878, which disclosure isspecifically incorporated herein by reference, and include one or moreof:

-   -   (a) DNA that includes at least one anti-sense DNA segment that        is anti-sense to at least one segment of the gene to be        suppressed;    -   (b) DNA that includes multiple copies of at least one anti-sense        DNA segment that is anti-sense to at least one segment of the        gene to be suppressed;    -   (c) DNA that includes at least one sense DNA segment that is at        least one segment of the gene to be suppressed;    -   (d) DNA that includes multiple copies of at least one sense DNA        segment that is at least one segment of the gene to be        suppressed;    -   (e) DNA that transcribes to RNA for suppressing the gene to be        suppressed by forming double-stranded RNA and includes at least        one anti-sense DNA segment that is anti-sense to at least one        segment of the gene to be suppressed and at least one sense DNA        segment that is at least one segment of the gene to be        suppressed;    -   (f) DNA that transcribes to RNA for suppressing the gene to be        suppressed by forming a single double-stranded RNA and includes        multiple serial anti-sense DNA segments that are anti-sense to        at least one segment of the gene to be suppressed and multiple        serial sense DNA segments that are at least one segment of the        gene to be suppressed;    -   (g) DNA that transcribes to RNA for suppressing the gene to be        suppressed by forming multiple double strands of RNA and        includes multiple anti-sense DNA segments that are anti-sense to        at least one segment of the gene to be suppressed and multiple        sense DNA segments that are at least one segment of the gene to        be suppressed, and wherein the multiple anti-sense DNA segments        and the multiple sense DNA segments are arranged in a series of        inverted repeats;    -   (h) DNA that includes nucleotides derived from a plant miRNA;    -   (i) DNA that includes nucleotides of a siRNA;    -   (j) DNA that transcribes to an RNA aptamer capable of binding to        a ligand; and    -   (k) DNA that transcribes to an RNA aptamer capable of binding to        a ligand, and DNA that transcribes to regulatory RNA capable of        regulating expression of the gene to be suppressed, wherein the        regulation is dependent on the conformation of the regulatory        RNA, and the conformation of the regulatory RNA is        allosterically affected by the binding state of the RNA aptamer.

In some embodiments, an intron is used to deliver a gene suppressionelement in the absence of any protein-coding exons (coding sequence). Inone example, an intron, such as an expression-enhancing intron(preferred in certain embodiments), is interrupted by embedding withinthe intron a gene suppression element, wherein, upon transcription, thegene suppression element is excised from the intron. Thus,protein-coding exons are not required to provide the gene suppressingfunction of the recombinant DNA constructs disclosed herein.

Transcription Regulatory Elements

In some embodiments, the recombinant DNA construct or polynucleotide ofthis invention includes DNA encoding a transcription regulatory element.Transcription regulatory elements include elements that regulate theexpression level of the recombinant DNA construct of this invention(relative to its expression in the absence of such regulatory elements).Examples of suitable transcription regulatory elements includeriboswitches (cis- or trans-acting), transcript stabilizing sequences,and miRNA recognition sites, as described in detail in U.S. PatentApplication Publication 2006/0200878, specifically incorporated hereinby reference.

Making and Using Transgenic Plant Cells and Transgenic Plants

Transformation of a plant can include any of several well-known methodsand compositions. Suitable methods for plant transformation includevirtually any method by which DNA can be introduced into a cell. Onemethod of plant transformation is microprojectile bombardment, forexample, as illustrated in U.S. Pat. No. 5,015,580 (soybean), U.S. Pat.No. 5,538,880 (maize), U.S. Pat. No. 5,550,318 (maize), U.S. Pat. No.5,914,451 (soybean), U.S. Pat. No. 6,153,812 (wheat), U.S. Pat. No.6,160,208 (maize), U.S. Pat. No. 6,288,312 (rice), U.S. Pat. No.6,365,807 (rice), and U.S. Pat. No. 6,399,861 (maize), and U.S. Pat. No.6,403,865 (maize), all of which are incorporated by reference forenabling the production of transgenic plants.

Another useful method of plant transformation is Agrobacterium-mediatedtransformation by means of Agrobacterium containing a binary Ti plasmidsystem, wherein the Agrobacterium carries a first Ti plasmid and asecond, chimeric plasmid containing at least one T-DNA border of awild-type Ti plasmid, a promoter functional in the transformed plantcell and operably linked to a polynucleotide or recombinant DNAconstruct of this invention. See, for example, the binary systemdescribed in U.S. Pat. No. 5,159,135, incorporated by reference. Alsosee De Framond (1983) Biotechnology, 1:262-269; and Hoekema et al.,(1983) Nature, 303:179. In such a binary system, the smaller plasmid,containing the T-DNA border or borders, can be conveniently constructedand manipulated in a suitable alternative host, such as E. coli, andthen transferred into Agrobacterium.

Detailed procedures for Agrobacterium-mediated transformation of plants,especially crop plants, include procedures disclosed in U.S. Pat. Nos.5,004,863, 5,159,135, and 5,518,908 (cotton); U.S. Pat. Nos. 5,416,011,5,569,834, 5,824,877 and 6,384,301 (soybean); U.S. Pat. Nos. 5,591,616and 5,981,840 (maize); 5,463,174 (brassicas including canola), 7,026,528(wheat), and 6,329,571 (rice), and in U.S. Patent ApplicationPublications 2004/0244075 (maize) and 2001/0042257 A1 (sugar beet), allof which are specifically incorporated by reference for enabling theproduction of transgenic plants. U.S. Patent Application Publication2011/0296555 discloses in Example 5 the transformation vectors(including the vector sequences) and detailed protocols for transformingmaize, soybean, canola, cotton, and sugarcane) and is specificallyincorporated by reference for enabling the production of transgenicplants. Similar methods have been reported for many plant species, bothdicots and monocots, including, among others, peanut (Cheng et al.(1996) Plant Cell Rep., 15: 653); asparagus (Bytebier et al. (1987)Proc. Natl. Acad. Sci. U.S.A., 84:5345); barley (Wan and Lemaux (1994)Plant Physiol., 104:37); rice (Toriyama et al. (1988) Bio/Technology,6:10; Zhang et al. (1988) Plant Cell Rep., 7:379; wheat (Vasil et al.(1992) Bio/Technology, 10:667; Becker et al. (1994) Plant J., 5:299),alfalfa (Masoud et al. (1996) Transgen. Res., 5:313); and tomato (Sun etal. (2006) Plant Cell Physiol., 47:426-431). See also a description ofvectors, transformation methods, and production of transformedArabidopsis thaliana plants where transcription factors areconstitutively expressed by a CaMV35S promoter, in U.S. PatentApplication Publication 2003/0167537 A1, incorporated by reference.Various methods of transformation of other plant species are well knownin the art, see, for example, the encyclopedic reference, “Compendium ofTransgenic Crop Plants”, edited by Chittaranjan Kole and Timothy C.Hall, Blackwell Publishing Ltd., 2008; ISBN 978-1-405-16924-0 (availableelectronically atmrw.interscience.wiley.com/emrw/9781405181099/hpt/toc), which describestransformation procedures for cereals and forage grasses (rice, maize,wheat, barley, oat, sorghum, pearl millet, finger millet, cool-seasonforage grasses, and bahiagrass), oilseed crops (soybean, oilseedbrassicas, sunflower, peanut, flax, sesame, and safflower), legumegrains and forages (common bean, cowpea, pea, faba bean, lentil, teparybean, Asiatic beans, pigeonpea, vetch, chickpea, lupin, alfalfa, andclovers), temperate fruits and nuts (apple, pear, peach, plums, berrycrops, cherries, grapes, olive, almond, and Persian walnut), tropicaland subtropical fruits and nuts (citrus, grapefruit, banana andplantain, pineapple, papaya, mango, avocado, kiwifruit, passionfruit,and persimmon), vegetable crops (tomato, eggplant, peppers, vegetablebrassicas, radish, carrot, cucurbits, alliums, asparagus, and leafyvegetables), sugar, tuber, and fiber crops (sugarcane, sugar beet,stevia, potato, sweet potato, cassava, and cotton), plantation crops,ornamentals, and turf grasses (tobacco, coffee, cocoa, tea, rubber tree,medicinal plants, ornamentals, and turf grasses), and forest treespecies One of ordinary skill in the art has various transformationmethodologies for production of stable transgenic plants.

Transformation methods to provide transgenic plant cells and transgenicplants containing stably integrated recombinant DNA are preferablypracticed in tissue culture on media and in a controlled environment.“Media” refers to the numerous nutrient mixtures that are used to growcells in vitro, that is, outside of the intact living organism.Recipient cell targets include, but are not limited to, meristem cells,callus, immature embryos or parts of embryos, and gametic cells such asmicrospores, pollen, sperm, and egg cells. Any cell from which a fertileplant can be regenerated is contemplated as a useful recipient cell forpractice of this invention. Callus can be initiated from various tissuesources, including, but not limited to, immature embryos or parts ofembryos, seedling apical meristems, microspores, and the like. Thosecells which are capable of proliferating as callus can serve asrecipient cells for genetic transformation. Practical transformationmethods and materials for making transgenic plants of this invention (e.g., various media and recipient target cells, transformation of immatureembryos, and subsequent regeneration of fertile transgenic plants) aredisclosed, for example, in U.S. Pat. Nos. 6,194,636 and 6,232,526 andU.S. Patent Application Publication 2004/0216189, which are specificallyincorporated by reference.

In general transformation practice, DNA is introduced into only a smallpercentage of target cells in any one transformation experiment. Markergenes are generally used to provide an efficient system foridentification of those cells that are stably transformed by receivingand integrating a transgenic DNA construct into their genomes. Preferredmarker genes provide selective markers which confer resistance to aselective agent, such as an antibiotic or herbicide. Any of theantibiotics or herbicides to which a plant cell is resistant can be auseful agent for selection. Potentially transformed cells are exposed tothe selective agent. In the population of surviving cells will be thosecells where, generally, the resistance-conferring gene is integrated andexpressed at sufficient levels to permit cell survival. Cells can betested further to confirm stable integration of the recombinant DNA.Commonly used selective marker genes include those conferring resistanceto antibiotics such as kanamycin or paromomycin (nptII), hygromycin B(aph IV) and gentamycin (aac3 and aacC4) or resistance to herbicidessuch as glufosinate (bar or pat) and glyphosate (EPSPS). Examples ofuseful selective marker genes and selection agents are illustrated inU.S. Pat. Nos. 5,550,318, 5,633,435, 5,780,708, and 6,118,047, all ofwhich are specifically incorporated by reference. Screenable markers orreporters, such as markers that provide an ability to visually identifytransformants can also be employed. Examples of useful screenablemarkers include, for example, a gene expressing a protein that producesa detectable color by acting on a chromogenic substrate (e. g., betaglucuronidase (GUS) (uidA) or luciferase (luc)) or that itself isdetectable, such as green fluorescent protein (GFP) (gfp) or animmunogenic molecule. Those of skill in the art will recognize that manyother useful markers or reporters are available for use.

Detecting or measuring transcription of a recombinant DNA construct in atransgenic plant cell can be achieved by any suitable method, includingprotein detection methods (e. g., western blots, ELISAs, and otherimmunochemical methods), measurements of enzymatic activity, or nucleicacid detection methods (e. g., Southern blots, northern blots, PCR,RT-PCR, fluorescent in situ hybridization).

Other suitable methods for detecting or measuring transcription in aplant cell of a recombinant polynucleotide of this invention targeting aDiabrotica species target gene include measurement of any other traitthat is a direct or proxy indication of the level of expression of thetarget gene in the Diabrotica species, relative to the level ofexpression observed in the absence of the recombinant polynucleotide, e.g., growth rates, mortality rates, or reproductive or recruitment ratesof the Diabrotica species, or measurements of injury (e. g., rootinjury) or yield loss in a plant or field of plants infested by theDiabrotica species. In general, suitable methods for detecting ormeasuring transcription in a plant cell of a recombinant polynucleotideof interest include, e. g., gross or microscopic morphological traits,growth rates, yield, reproductive or recruitment rates, resistance topests or pathogens, or resistance to biotic or abiotic stress (e. g.,water deficit stress, salt stress, nutrient stress, heat or coldstress). Such methods can use direct measurements of a phenotypic traitor proxy assays (e. g., in plants, these assays include plant partassays such as leaf or root assays to determine tolerance of abioticstress). Such methods include direct measurements of resistance to aninvertebrate pest or pathogen (e. g., damage to plant tissues) or proxyassays (e. g., plant yield assays, or bioassays such as the Western cornrootworm (Diabrotica virgifera virgifera LeConte) larval bioassaydescribed in International Patent Application Publication WO2005/110068A2 and U.S. Patent Application Publication US 2006/0021087 A1,specifically incorporated by reference, or the soybean cyst nematodebioassay described by Steeves et al. (2006) Funct. Plant Biol.,33:991-999, wherein cysts per plant, cysts per gram root, eggs perplant, eggs per gram root, and eggs per cyst are measured.

The recombinant DNA constructs of this invention can be stacked withother recombinant DNA for imparting additional traits (e. g., in thecase of transformed plants, traits including herbicide resistance, pestresistance, cold germination tolerance, water deficit tolerance, and thelike) for example, by expressing or suppressing other genes. Constructsfor coordinated decrease and increase of gene expression are disclosedin U.S. Patent Application Publication 2004/0126845 A1, specificallyincorporated by reference.

Seeds of fertile transgenic plants can be harvested and used to growprogeny generations, including hybrid generations, of transgenic plantsof this invention that include the recombinant DNA construct in theirgenome. Thus, in addition to direct transformation of a plant with arecombinant DNA construct of this invention, transgenic plants of thisinvention can be prepared by crossing a first plant having therecombinant DNA with a second plant lacking the construct. For example,the recombinant DNA can be introduced into a plant line that is amenableto transformation to produce a transgenic plant, which can be crossedwith a second plant line to introgress the recombinant DNA into theresulting progeny. A transgenic plant of this invention can be crossedwith a plant line having other recombinant DNA that confers one or moreadditional trait(s) (such as, but not limited to, herbicide resistance,pest or disease resistance, environmental stress resistance, modifiednutrient content, and yield improvement) to produce progeny plantshaving recombinant DNA that confers both the desired target sequenceexpression behavior and the additional trait(s).

In such breeding for combining traits the transgenic plant donating theadditional trait can be a male line (pollinator) and the transgenicplant carrying the base traits can be the female line. The progeny ofthis cross segregate such that some of the plant will carry the DNA forboth parental traits and some will carry DNA for one parental trait;such plants can be identified by markers associated with parentalrecombinant DNA Progeny plants carrying DNA for both parental traits canbe crossed back into the female parent line multiple times, e. g.,usually 6 to 8 generations, to produce a homozygous progeny plant withsubstantially the same genotype as one original transgenic parental lineas well as the recombinant DNA of the other transgenic parental line.

Yet another aspect of this invention is a transgenic plant grown fromthe transgenic seed of this invention. This invention contemplatestransgenic plants grown directly from transgenic seed containing therecombinant DNA as well as progeny generations of plants, includinginbred or hybrid plant lines, made by crossing a transgenic plant growndirectly from transgenic seed to a second plant not grown from the sametransgenic seed. Crossing can include, for example, the following steps:

-   -   (a) plant seeds of the first parent plant (e. g., non-transgenic        or a transgenic) and a second parent plant that is transgenic        according to the invention;    -   (b) grow the seeds of the first and second parent plants into        plants that bear flowers;    -   (c) pollinate a flower from the first parent with pollen from        the second parent; and    -   (d) harvest seeds produced on the parent plant bearing the        fertilized flower.

It is often desirable to introgress recombinant DNA into elitevarieties, e. g., by backcrossing, to transfer a specific desirabletrait from one source to an inbred or other plant that lacks that trait.This can be accomplished, for example, by first crossing a superiorinbred (“A”) (recurrent parent) to a donor inbred (“B”) (non-recurrentparent), which carries the appropriate gene(s) for the trait inquestion, for example, a construct prepared in accordance with thecurrent invention. The progeny of this cross first are selected in theresultant progeny for the desired trait to be transferred from thenon-recurrent parent “B”, and then the selected progeny are mated backto the superior recurrent parent “A”. After five or more backcrossgenerations with selection for the desired trait, the progeny can beessentially hemizygous for loci controlling the characteristic beingtransferred, but are like the superior parent for most or almost allother genes. The last backcross generation would be selfed to giveprogeny which are pure breeding for the gene(s) being transferred, i.e., one or more transformation events.

Through a series of breeding manipulations, a selected DNA construct canbe moved from one line into an entirely different line without the needfor further recombinant manipulation. One can thus produce inbred plantswhich are true breeding for one or more DNA constructs. By crossingdifferent inbred plants, one can produce a large number of differenthybrids with different combinations of DNA constructs. In this way,plants can be produced which have the desirable agronomic propertiesfrequently associated with hybrids (“hybrid vigor”), as well as thedesirable characteristics imparted by one or more DNA constructs.

In certain transgenic plant cells and transgenic plants of thisinvention, it is sometimes desirable to concurrently express a gene ofinterest while also modulating expression of a Diabrotica target gene.Thus, in some embodiments, the transgenic plant contains recombinant DNAfurther including a gene expression element for expressing at least onegene of interest, and transcription of the recombinant DNA construct ofthis invention is preferably effected with concurrent transcription ofthe gene expression element.

In some embodiments, the recombinant DNA constructs of this inventioncan be transcribed in any plant cell or tissue or in a whole plant ofany developmental stage. Transgenic plants can be derived from anymonocot or dicot plant, such as, but not limited to, plants ofcommercial or agricultural interest, such as crop plants (especiallycrop plants used for human food or animal feed), wood- or pulp-producingtrees, vegetable plants, fruit plants, and ornamental plants. Examplesof plants of interest include grain crop plants (such as wheat, oat,barley, maize, rye, triticale, rice, millet, sorghum, quinoa, amaranth,and buckwheat); forage crop plants (such as forage grasses and foragedicots including alfalfa, vetch, clover, and the like); oilseed cropplants (such as cotton, safflower, sunflower, soybean, canola, rapeseed,flax, peanuts, and oil palm); tree nuts (such as walnut, cashew,hazelnut, pecan, almond, and the like); sugarcane, coconut, date palm,olive, sugarbeet, tea, and coffee; wood- or pulp-producing trees;vegetable crop plants such as legumes (for example, beans, peas,lentils, alfalfa, peanut), lettuce, asparagus, artichoke, celery,carrot, radish, the brassicas (for example, cabbages, kales, mustards,and other leafy brassicas, broccoli, cauliflower, Brussels sprouts,turnip, kohlrabi), edible cucurbits (for example, cucumbers, melons,summer squashes, winter squashes), edible alliums (for example, onions,garlic, leeks, shallots, chives), edible members of the Solanaceae (forexample, tomatoes, eggplants, potatoes, peppers, groundcherries), andedible members of the Chenopodiaceae (for example, beet, chard, spinach,quinoa, amaranth); fruit crop plants such as apple, pear, citrus fruits(for example, orange, lime, lemon, grapefruit, and others), stone fruits(for example, apricot, peach, plum, nectarine), banana, pineapple,grape, kiwifruit, papaya, avocado, and berries; plants grown for biomassor biofuel (for example, Miscanthus grasses, switchgrass, jatropha, oilpalm, eukaryotic microalgae such as Botryococcus braunii, Chlorellaspp., and Dunaliella spp., and eukaryotic macroalgae such as Gracilariaspp., and Sargassum spp.); and ornamental plants including ornamentalflowering plants, ornamental trees and shrubs, ornamental groundcovers,and ornamental grasses.

This invention also provides commodity products produced from atransgenic plant cell, plant, or seed of this invention, including, butnot limited to, harvested leaves, roots, shoots, tubers, stems, fruits,seeds, or other parts of a plant, meals, oils, extracts, fermentation ordigestion products, crushed or whole grains or seeds of a plant, or anyfood or non-food product including such commodity products produced froma transgenic plant cell, plant, or seed of this invention. The detectionof one or more of nucleic acid sequences of the recombinant DNAconstructs of this invention in one or more commodity or commodityproducts contemplated herein is de facto evidence that the commodity orcommodity product contains or is derived from a transgenic plant cell,plant, or seed of this invention.

Generally a transgenic plant having in its genome a recombinant DNAconstruct of this invention exhibits increased resistance to aDiabrotica species infestation. In various embodiments, for example,where the transgenic plant expresses a recombinant DNA construct of thisinvention that is stacked with other recombinant DNA for impartingadditional traits, the transgenic plant has at least one additionalaltered trait, relative to a plant lacking the recombinant DNAconstruct, selected from the group of traits consisting of:

-   -   (a) improved abiotic stress tolerance;    -   (b) improved biotic stress tolerance;    -   (c) modified primary metabolite composition;    -   (d) modified secondary metabolite composition;    -   (e) modified trace element, carotenoid, or vitamin composition;    -   (f) improved yield;    -   (g) improved ability to use nitrogen, phosphate, or other        nutrients;    -   (h) modified agronomic characteristics;    -   (i) modified growth or reproductive characteristics; and    -   (j) improved harvest, storage, or processing quality.

In some embodiments, the transgenic plant is characterized by: improvedtolerance of abiotic stress (e. g., tolerance of water deficit ordrought, heat, cold, non-optimal nutrient or salt levels, non-optimallight levels) or of biotic stress (e. g., crowding, allelopathy, orwounding); by a modified primary metabolite (e. g., fatty acid, oil,amino acid, protein, sugar, or carbohydrate) composition; a modifiedsecondary metabolite (e. g., alkaloids, terpenoids, polyketides,non-ribosomal peptides, and secondary metabolites of mixed biosyntheticorigin) composition; a modified trace element (e. g., iron, zinc),carotenoid (e. g., beta-carotene, lycopene, lutein, zeaxanthin, or othercarotenoids and xanthophylls), or vitamin (e. g., tocopherols)composition; improved yield (e. g., improved yield under non-stressconditions or improved yield under biotic or abiotic stress); improvedability to use nitrogen, phosphate, or other nutrients; modifiedagronomic characteristics (e. g., delayed ripening; delayed senescence;earlier or later maturity; improved shade tolerance; improved resistanceto root or stalk lodging; improved resistance to “green snap” of stems;modified photoperiod response); modified growth or reproductivecharacteristics (e. g., intentional dwarfing; intentional malesterility, useful, e. g., in improved hybridization procedures; improvedvegetative growth rate; improved germination; improved male or femalefertility); improved harvest, storage, or processing quality (e. g.,improved resistance to pests during storage, improved resistance tobreakage, improved appeal to consumers); or any combination of thesetraits.

In another embodiment, transgenic seed, or seed produced by thetransgenic plant, has modified primary metabolite (e. g., fatty acid,oil, amino acid, protein, sugar, or carbohydrate) composition, amodified secondary metabolite composition, a modified trace element,carotenoid, or vitamin composition, an improved harvest, storage, orprocessing quality, or a combination of these. In another embodiment, itcan be desirable to change levels of native components of the transgenicplant or seed of a transgenic plant, for example, to decrease levels ofan allergenic protein or glycoprotein or of a toxic metabolite.

Generally, screening a population of transgenic plants each regeneratedfrom a transgenic plant cell is performed to identify transgenic plantcells that develop into transgenic plants having the desired trait. Thetransgenic plants are assayed to detect an enhanced trait, e. g.,enhanced water use efficiency, enhanced cold tolerance, increased yield,enhanced nitrogen use efficiency, enhanced seed protein, and enhancedseed oil. Screening methods include direct screening for the trait in agreenhouse or field trial or screening for a surrogate trait. Suchanalyses are directed to detecting changes in the chemical composition,biomass, physiological properties, or morphology of the plant. Changesin chemical compositions such as nutritional composition of grain aredetected by analysis of the seed composition and content of protein,free amino acids, oil, free fatty acids, starch, tocopherols, or othernutrients. Changes in growth or biomass characteristics are detected bymeasuring plant height, stem diameter, internode length, root and shootdry weights, and (for grain-producing plants such as maize, rice, orwheat) ear or seed head length and diameter. Changes in physiologicalproperties are identified by evaluating responses to stress conditions,e. g., assays under imposed stress conditions such as water deficit,nitrogen or phosphate deficiency, cold or hot growing conditions,pathogen or insect attack, light deficiency, or increased plant density.Other selection properties include days to pollen shed, days to silkingin maize, leaf extension rate, chlorophyll content, leaf temperature,stand, seedling vigor, internode length, plant height, leaf number, leafarea, tillering, brace roots, staying green, stalk lodging, rootlodging, plant health, fertility, green snap, and pest resistance. Inaddition, phenotypic characteristics of harvested seed can be evaluated;for example, in maize this can include the number of kernels per row onthe ear, number of rows of kernels on the ear, kernel abortion, kernelweight, kernel size, kernel density and physical grain quality. Thefollowing illustrates examples of screening assays useful foridentifying desired traits in maize plants. These can be readily adaptedfor screening other plants such as canola, cotton, and soybean either ashybrids or inbreds.

Transgenic maize plants having nitrogen use efficiency are identified byscreening in fields with three levels of nitrogen fertilizer beingapplied, e. g., low level (0 pounds/acre), medium level (80 pounds/acre)and high level (180 pounds/acre). Plants with enhanced nitrogen useefficiency provide higher yield as compared to control plants.

Transgenic maize plants having enhanced yield are identified byscreening the transgenic plants over multiple locations with plantsgrown under optimal production management practices and maximum weed andpest control. A useful target for improved yield is a 5% to 10% increasein yield as compared to yield produced by plants grown from seed for acontrol plant. Selection methods can be applied in multiple and diversegeographic locations and over one or more planting seasons tostatistically distinguish yield improvement from natural environmentaleffects.

Transgenic maize plants having enhanced water use efficiency areidentified by screening plants in an assay where water is withheld forperiod to induce stress followed by watering to revive the plants. Forexample, a useful selection process imposes 3 drought/re-water cycles onplants over a total period of 15 days after an initial stress freegrowth period of 11 days. Each cycle consists of 5 days, with no waterbeing applied for the first four days and a water quenching on the 5thday of the cycle. The primary phenotypes analyzed by the selectionmethod are the changes in plant growth rate as determined by height andbiomass during a vegetative drought treatment.

Transgenic maize plants having enhanced cold tolerance are identified byscreening plants in a cold germination assay and/or a cold tolerancefield trial. In a cold germination assay trays of transgenic and controlseeds are placed in a dark growth chamber at 9.7 degrees Celsius for 24days. Seeds having higher germination rates as compared to the controlare identified as having enhanced cold tolerance. In a cold tolerancefield trial plants with enhanced cold tolerance are identified fromfield planting at an earlier date than conventional spring planting forthe field location. For example, seeds are planted into the groundaround two weeks before local farmers begin to plant maize so that asignificant cold stress is exerted onto the crop. As a control, seedsalso are planted under local optimal planting conditions such that thecrop has little or no exposure to cold condition. At each location,seeds are planted under both cold and normal conditions preferably withmultiple repetitions per treatment.

EXAMPLES Example 1

This example illustrates non-limiting embodiments of sequences useful astarget genes for controlling Diabrotica species and for makingcompositions and plants of this invention, and describes identificationof such DNA sequences from Diabrotica virgifera virgifera. It isrecognized that analogous sequences can be obtained from any otherDiabrotica species referred to hereinabove.

cDNA libraries were generated from mid-guts of Diabrotica virgiferavirgifera (Western corn rootworm, WCR) third instar larvae reared oncorn plants, as follows. Disinfected WCR eggs were suspended in a 0.1%(w/v) agar solution and dispensed into petri dishes containing 2% (w/v)agar and filter paper. The WCR eggs were incubated first at 20 degreesCelsius and 60% relative humidity (“RH”) for 3 days and then at 25degrees Celsius and 60% RH for 10 days. After 13 days of incubation, theeggs were washed from the dishes into sweater boxes containing soil (2parts Metro-Mix 200: 1 part Redi-Earth; steam-sterilized) and germinatedcorn mats, which were prepared by geminating corn seeds of Dekalb lineDKC64-04 in sweater boxes containing germination paper wet with 1.0%(w/v) 3336F fungicide. Larvae were reared in sweater boxes in a growthchamber (25 degrees Celsius, 70% relative humidity, irrigated for 10minutes every 2 days, and fertilized every 4 days). Third instar larvaewere dissected to separate mid-guts from other body parts (cuticle,head, fore- and hind-gut, and fat body). The harvested mid-guts wereplaced in chilled microcentrifuge tubes with 25 millimolar Tris buffer(pH 7.4), thoroughly saturated with the buffer, and then centrifuged for5 minutes at 14,000 g at 4 degrees Celsius. The supernatant wasdiscarded and mid-gut pellets were immediately frozen in liquid nitrogenand stored at −80 degrees Celsius until used for total RNA preparation.Total RNA was purified, from which the cDNA library was obtained byhigh-throughput sequencing using commercially available 454 technology(454 Life Sciences, 15 Commercial St., Branford, Conn. 06405, USA), asdescribed in Margulies et al. (2005) Nature, 437:376-380. This providedapproximately 1.27 million ˜300 base-pair reads, which were supplementedwith 17,800 publicly available ˜520 base-pair Sanger reads from NCBI.The combined sequence data were assembled into contigs de novo using theNewbler (version 2.3) software package (454 Life Sciences, 15 CommercialSt., Branford, Conn. 06405, USA). Approximately 16,130 genes wereidentified from the assembled sequence data.

Example 2

This example illustrates a method for non-random selection of targetgenes. More specifically, this example illustrates a method of selectinga subset of target genes that are present in single- or low-copy-number(i. e., non-repetitive and non-redundant) in a particular genome.

In general the method includes the step of identifying single- orlow-copy-number genes in the chosen genome, or alternatively to identifysingle- or low-copy-number genes in an orthologous database from relatedorganisms to predict which genes will be single/low copy in the chosenorganism. Low-copy genes, and in particular single-copy genes, areunlikely to have their function recapitulated by a paralogue, and areselected as preferred targets for RNAi-mediated silencing. In otherwords, such genes are likely to represent essential functions, makingthese genes preferred targets for RNAi-mediated silencing.

Embodiments of the method include a further step of estimatingnucleotide diversity for low-/single-copy gene in a population of thechosen organism and selecting those low-/single-copy genes that furtherhave the lowest nucleotide diversity. Low-/single-copy genes thatfurther have low nucleotide diversity are selected as preferred targetsfor RNAi-mediated silencing. One advantage provided by this step issimplification of design of recombinant nucleotide sequences (e. g.,recombinant dsRNA sequences) for silencing such genes, as thepossibility of mismatches between the silencing polynucleotide and thetarget gene is decreased.

Embodiments of the method include a further step of comparing the ratioof synonymous (K_(s)) to nonsynonymous (K_(a)) nucleotide changes as anestimate of functional or evolutionary constraint. If mutation occurs atrandom, for a gene randomly made of all possible codons, K_(a) isapproximately 2 times greater than K_(s), given the structure of thegenetic code. For genes under strong functional constraints (i. e.,those genes likely to decrease fitness of the source organism if genefunctionality is lost), natural selection is expected to removenonsynonymous changes from the population while tolerating synonymousones, resulting in a shift of the observed substitutions towardK_(s)>K_(a). Selection of target genes can therefore be improved byincluding an estimate of functional or evolutionary constraint byselecting genes where K_(s)>>K_(a).

In a non-limiting example of the method, a public database oforthologous genes, OrthoDB6 (available at cegg.unige.ch/orthodb6 anddescribed in Waterhouse et al. (2012) Nucleic Acids Res., PMID:23180791)was filtered to select a subset of 450 genes that were single-copy inTribolium castaneum (red flour beetle, a coleopteran species) as well assingle-copy in all available arthropod genomes in the database (i. e.,33 other arthropod genomes available at the time this application isfiled).

While Diabrotica virgifera virgifera is not included in the OrthoDBdatabase, Tribolium castaneum is a coleopteran species and is thereforemore closely related to Diabrotica species than to other species in thedatabase, which makes it more likely that a single-copy gene present inthe Tribolium castaneum genome database will also be a single-copy genein the Diabrotica virgifera virgifera genome, at least for genes thathave high sequence similarity in the two organisms. From the 16,130sequence contigs obtained from the Diabrotica virgifera virgifera(Western corn rootworm, WCR) sequencing and assembly described inExample 1, a subset of 450 genes were identified using a translatednucleotide BLAST search (tblastx) as genes having high sequencesimilarity (significance or e-value of less than or equal to 1×10⁻¹⁵) tothe 450 single-copy Tribolium castaneum genes in the OrthoDB database.

For sequence annotation, SmartBlast annotation was performed by usingNCBI's Blastall 2.2.21 software to search Diabrotica virgifera virgiferacontigs against the publicly available uniref90.fasta database(ftp.uniprot.org/pub/databases/uniprot/current_release/uniref/uniref90/).The blast search was performed in blastx mode (translated Diabroticavirgifera virgifera nucleotide queries searched against the uniref90protein database). Only blast hits with an e-value less than or equal to9e-9 were retained. For each Diabrotica virgifera virgifera contig thedescription line from the uniref90 best hit was used as an annotation.When no SmartBlast hits were found, the sequence was subjected to asupplementary Pfam search. To accomplish this, the longest open readingframe (ORF) was identified for each Diabrotica virgifera virgiferacontig and used to query the publicly available Pfam-A database(ftp.sanger.ac.uk/pub/databases/Pfam/current_release) using the publiclyavailable HMMER 3.0 software package (hmmer.janelia.org/). Diabroticavirgifera virgifera contigs with a Pfam hit with an e-value less than orequal to 1e-5 were annotated with the protein family name and the Pfamidentifier. Diabrotica virgifera virgifera contigs with no SmartBlast orPfam hit were annotated as “novel protein”.

The subset of 450 Diabrotica virgifera virgifera genes is provided inTable 1, with each gene annotated based on sequence similarity toTribolium castaneum and/or OrthoDB sequences, or by conserved Pfamdomains. For each Diabrotica virgifera virgifera gene, the correspondingTribolium castaneum presumed homologous single-copy gene is alsoidentified, together with the similarity e-value for each pair.

TABLE 1 Tribolium Blast E- Gene value Name Tribolium from Gene vs SEQOrthoDB Diabrotica ID NO. Annotation database Unigene 1 Sorting nexin-6TC000458 0 2 Alpha spectrin TC000749 0 3 Clathrin TC015014 0 4Eukaryotic translation initiation factor 3 subunit, putative TC012303 05 Lipin TC010029 0 6 Phagocyte signaling-impaired protein TC015420 0 7Coatomer subunit beta′, putative TC013867 0 8 Ns1 binding proteinTC009594 0 9 Eukaryotic translation initiation factor 3 subunit BTC006009 0 10 TTC27 protein TC011547 0 11 Lissencephaly-1 homologTC005496 0 12 Wd-repeat protein TC005722 0 13 Glutaminyl-trna synthetaseTC000042 0 14 Transcription factor 25 TC030734 0 15Sphingosine-1-phosphate lyase TC000875 0 16 Cleft lip and palatetransmembrane protein TC008245 0 17 Vesicle docking protein P115TC006352 0 18 Glutaminase kidney isoform, mitochondrial TC004628 0 19eukaryotic translation initiation factor 2A TC013517 0 20 T-complexprotein 1 subunit delta TC007791 0 21 ATP-grasp enzyme-like proteinTC000357 0 22 Fimbrin TC001769 0 23 Pyridoxal-dependent decarboxylasedomain-containing protein 1 TC005445 0 24 Coatomer subunit delta(Fragment) TC003020 0 25 Putative phosphoglycerate kinase TC015540 0 26Glycylpeptide N-tetradecanoyltransferase 2 TC015649 0 27Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, putative TC011712 0 28Sly1 protein-like protein TC007530 0 29 Trifunctional enzyme betasubunit (Tp-beta) TC008872 0 30 Zgc: 100980 TC006359 0 31 26S proteasomenon-ATPase regulatory subunit 3 TC014286 0 32 26S proteasome non-ATPaseregulatory subunit, putative TC006260 0 33 Pre-mRNA-processing factor 6TC005794 0 34 Sodium-dependent phosphate transport protein 1,chloroplastic TC015307 0 35 Protein singed, putative TC006673 0 36WD-repeat protein, putative TC001051 3.00E−180 37 Eukaryotic translationinitiation factor 3 subunit H TC014327 7.00E−180 38 SWI/SNF-relatedmatrix-associated actin-dependent regulator of TC012873 1.00E−179chromatin subfamily D member 1 39 26S proteasome non-ATPase regulatorysubunit, putative TC015728 1.00E−178 40 Elongation factor 1-gammaTC007229 2.00E−175 41 Abhydrolase domain-containing protein 2 TC0097699.00E−171 42 Transmembrane protein 184B TC003325 9.00E−171 43 PelotaTC001682 3.00E−170 44 DNA polymerase epsilon, catalytic subunit TC0096003.00E−170 45 Polymerase delta-interacting protein 2 TC014911 3.00E−16746 Methylthioribose-1-phosphate isomerase TC002054 3.00E−166 47Chitobiosyldiphosphodolichol beta-mannosyltransferase TC003528 1.00E−16448 Failed axon connections protein, putative TC000100 3.00E−163 49Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kDaTC005188 2.00E−160 subunit, putative 50 Membrane-bound O-acyltransferasedomain-containing protein 2 TC030770 2.00E−158 51 Coproporphyrinogen iiioxidase TC000466 9.00E−158 52 Mitochondrial sulfide quinoneoxidoreductase TC001316 8.00E−157 53 Coiled-coil domain-containingprotein 47, putative TC005820 6.00E−153 54 Eukaryotic translationinitiation factor 2 subunit 1 TC010161 8.00E−151 55 Branched chainalpha-keto acid dehydrogenase E1 beta subunit TC000711 2.00E−150 56Zinc-type alcohol dehydrogenase-like protein C1773.06c TC0135671.00E−146 57 Ef-hand protein nucb1 TC003574 2.00E−145 58 Cxpwmw03TC004703 3.00E−145 59 Gerrochelatase, putative TC014202 8.00E−145 60D-3-phosphoglycerate dehydrogenase TC013082 1.00E−144 61Sphingosine-1-phosphate phosphatase 1 TC012252 2.00E−144 62Delta-aminolevulinic acid dehydratase TC009997 3.00E−143 63 ApyraseTC005356 3.00E−142 64 NADH dehydrogenase (Ubiquinone) 1 alphasubcomplex, 10 TC008030 4.00E−142 65 CDK5 and ABL1 enzyme substrate 1TC013369 2.00E−140 66 THO complex subunit 5-like protein TC0055386.00E−140 67 WD repeat-containing protein 75 TC003309 2.00E−139 68Oligopeptidase TC010332 3.00E−137 69 Sodium/bile acid cotransporter 7TC006130 6.00E−136 70 DCN1-like protein 1 (Fragment) TC013916 1.00E−13371 Zinc finger protein 330 homolog TC007558 2.00E−133 72Microfibrillar-associated protein TC000456 2.00E−132 73 Proliferatingcell nuclear antigen TC008874 2.00E−132 74 Solute carrier family 2,facilitated glucose transporter member 6 TC015433 3.00E−132 75 Prolyl3-hydroxylase 2 TC004700 8.00E−132 76 60S ribosomal protein L10,mitochondrial TC014453 6.00E−130 77 General transcription factor IIFsubunit 2 TC013555 1.00E−129 78 Electron transfer flavoprotein subunitbeta TC008707 5.00E−129 79 Zinc finger protein-like 1 TC009067 3.00E−12780 COMPASS component SWD2, putative TC014755 2.00E−126 81 Proteinphosphatase 2A, 59 kDa regulatory subunit B, putative TC009266 1.00E−12382 Translation initiation factor eIF-2B subunit delta TC008223 3.00E−12383 Nucleoporin seh1, putative TC009902 2.00E−122 84 Rho-associatedprotein kinase, putative TC011950 9.00E−122 85 Golgi resident proteinGCP60 TC007892 7.00E−120 86 Coatomer subunit epsilon TC001210 9.00E−12087 Suppressor of profilin 2 TC000050 1.00E−119 88 Nucleolar protein 10TC014492 1.00E−119 89 CCR4-NOT transcription complex subunit 3 TC0025012.00E−118 90 Nimrod B TC011428 7.00E−118 91 Probable splicing factor,arginine/serine-rich 7 TC009171 2.00E−116 92 Leo1-like protein; Pfam:PF04004 TC013564 3.00E−116 93 Vesicular mannose-binding lectin TC0125789.00E−116 94 Two pore calcium channel protein 1 TC015674 2.00E−115 9539S ribosomal protein L2, mitochondrial TC000434 6.00E−114 96 Zinctransporter 9 TC007348 9.00E−114 97 Cmp-sialic acid transporter TC0077031.00E−113 98 Sparc TC000930 2.00E−112 99 RGS-GAIP interacting proteinGIPC TC011711 3.00E−112 100 CG6672 TC015914 2.00E−110 101 DDB1- andCUL4-associated factor 7 TC012028 1.00E−109 102 Deoxyhypusine synthaseTC002446 2.00E−109 103 Ubiquitin domain-containing protein UBFD1TC003520 8.00E−109 104 Sorting nexin-4 TC000603 2.00E−108 105 ProbableGDP-mannose 4,6 dehydratase TC011606 3.00E−108 106 Lethal s1921 TC0067466.00E−107 107 Cytochrome c-type heme lyase TC011725 4.00E−105 108Vesicle-trafficking protein SEC22b TC007954 5.00E−105 109Vacuolar-sorting protein SNF8 TC007472 1.00E−103 110 Protein rogdiTC011795 1.00E−103 111 Probable GDP-fucose transporter TC0123261.00E−101 112 Slc39a9-prov protein TC015133 3.00E−101 113 Cysteinedesulfurylase TC014434 5.00E−101 114 ZIP Zinc transporter; Pfam: PF02535TC003468 1.00E−100 115 AN1-type zinc finger protein, putative TC0132511.00E−100 116 Blastoderm specific protein 25D, putative TC0035164.00E−99 117 Eukaryotic initiation factor 4E TC012945 2.00E−95 118Lysophospholipase TC011535 3.00E−95 119 Protein Red TC015452 3.00E−95120 ATP-dependent RNA helicase SUV3, mitochondrial TC012348 6.00E−95 121Vacuolar protein sorting-associated protein 11-like protein TC0055869.00E−95 122 Alpha-1,3-mannosyltransferase TC013994 8.00E−94 123Tubulin-specific chaperone C TC008402 2.00E−92 124 A kinase anchorprotein 10, mitochondrial TC012804 2.00E−92 125 Cop-coated vesiclemembrane protein P24 TC012624 3.00E−92 126 Transcription initiationfactor TFIID subunit 6 TC013033 5.00E−92 127 DnaJ-like protein subfamilyC member 10 TC000962 2.00E−91 128 GTP cyclohydrolase 1 TC010564 2.00E−91129 vesicle-mediated transport protein Vid24 TC006738 3.00E−91 130Transmembrane emp24 domain-containing protein 2 TC015633 5.00E−91 131Transmembrane protein 145 TC003142 5.00E−91 132UDP-N-acetylglucosamine--dolichyl-phosphate N- TC007854 1.00E−90acetylglucosaminephosphotransferase 133 CG8290, isoform B TC0083882.00E−90 134 Charged multivesicular body protein 2a TC007124 3.00E−90135 Cappuccino TC012258 3.00E−90 136 Protein MAK16-like protein ATC000795 1.00E−88 137 CG5131 TC003033 1.00E−88 138 Protein LTV1-likeprotein TC008848 3.00E−88 139 RING finger and CHY zinc fingerdomain-containing protein 1 TC009851 3.00E−88 140 Aspartyl/asparaginylbeta-hydroxylase TC001594 3.00E−88 141 Presenilin sel-12 TC0101781.00E−87 142 CG8108, isoform A TC003237 2.00E−87 143 NADH dehydrogenaseTC015022 3.00E−87 144 CAAX prenyl protease 2 TC008733 1.00E−86 145Adaptin ear-binding coat-associated protein 2 TC011619 5.00E−86 146Integrator complex subunit 3 TC002074 8.00E−86 147 Actin-related protein5 TC009219 1.00E−85 148 Etoposide-induced protein 2.4-like proteinTC008317 2.00E−85 149 Leucine-rich repeat flightless-interactingprotein, putative TC012376 3.00E−85 150 Tollip-like protein TC0071251.00E−84 151 Complement component TC010563 3.00E−84 152 Protein tyrosinephosphatase prl TC004794 5.00E−84 153 StAR-related lipid transferprotein 7 TC004819 5.00E−84 154 ETS translocation variant 1 TC0306511.00E−83 155 Peroxisomal biogenesis factor, putative TC002842 3.00E−83156 Ribosomal protein L12e TC010002 1.00E−82 157 Cellularretinaldehyde-binding protein TC005781 2.00E−82 158 Switch-associatedprotein 70 TC006709 2.00E−82 159 Helicase with zinc finger proteindomain helz, putative TC003141 2.00E−82 160 CG8315 TC009150 3.00E−82 161Sorting nexin TC000739 3.00E−82 162 WD repeat-containing protein SAZDTC006390 3.00E−82 163 Mannosyltransferase TC005068 6.00E−82 164Prefoldin subunit 3 TC001098 7.00E−82 165 Mediator of RNA polymerase IItranscription subunit 8 TC009839 7.00E−82 166 Nuclear distributionprotein NUDC TC015243 2.00E−81 167 CG1812, isoform A TC012393 2.00E−81168 Transmembrane BAX inhibitor motif-containing protein 4 TC0134293.00E−81 169 Alkylated DNA repair protein alkB-like protein 6 TC0007905.00E−81 170 Mitochondrial ribosomal protein, L45, putative TC0090235.00E−81 171 Myb-binding protein 1A TC015701 7.00E−81 172 ProteinLSM12-like protein TC015064 9.00E−81 173 Retrograde Golgi transportprotein RGP1-like protein TC009939 1.00E−80 174 Glucosamine-6-phosphateN-acetyltransferase TC009619 4.00E−80 175 ATPase family AAAdomain-containing protein 3 TC014695 5.00E−80 176 Tumor necrosis factorinduced protein TC004961 1.00E−79 177 Zinc finger CCHC domain-containingprotein 9 TC005967 2.00E−79 178 Prenylated Rab acceptor protein,putative TC014897 2.00E−79 179 Phd finger protein TC006094 2.00E−79 180Mitochondrial ribosomal protein L17 TC007726 4.00E−79 181 cAMP-dependentprotein kinase catalytic subunit, putative TC009500 1.00E−78 182 Tab2TC005952 1.00E−77 183 Polyadenylation factor subunit, putative TC0013521.00E−77 184 Vacuolar H+-ATPase v1 sector subunit E TC010367 3.00E−77185 Methyltransferase-like protein 10 TC003501 5.00E−77 186Dihydrofolate reductase TC030670 3.00E−76 187 tRNA(Guanine-N(7)-)-methyltransferase TC012665 3.00E−76 188 Thioredoxin-likeprotein 4A TC007987 2.00E−75 189 Flap endonuclease 1 TC009261 2.00E−75190 6-phosphogluconolactonase TC005667 3.00E−75 191 Mediator of RNApolymerase II transcription subunit 19 TC011979 3.00E−75 192 Putativemicrosomal signal peptidase 25 kD subunit TC013119 6.00E−75 193 RNA 3′terminal phosphate cyclase TC002529 6.00E−75 194 Ral guanine nucleotidedissociation stimulator-like 1 TC003754 7.00E−75 195 Cysteine-richhydrophobic protein TC012812 2.00E−74 196 WW domain-binding protein 2TC005552 5.00E−74 197 Ribosomal protein L21 TC007932 5.00E−74 198 CG8768TC003713 6.00E−74 199 HEAT repeat containing 7A isoform 2 TC0104318.00E−74 200 Peroxisomal biogenesis factor, putative TC015168 2.00E−72201 Tumor protein D54-like TC013379 5.00E−72 202 Zinc finger CCCHdomain-containing protein 15-like protein TC000028 8.00E−72 203 CG7864TC030620 9.00E−72 204 WD repeat-containing protein 47 TC001580 1.00E−71205 Galactose-1-phosphate uridylyltransferase TC003858 2.00E−71 206fibroblast growth factor (acidic) intracellular binding protein TC0060411.00E−70 207 Synaptic vesicle 2-related protein TC003566 5.00E−70 208Coiled-coil protein, putative TC001451 9.00E−70 209 F1-ATPase chaperoneTC006560 1.00E−69 210 NADH dehydrogenase, putative TC006357 1.00E−69 211COP9 signalosome complex subunit, putative TC030655 3.00E−69 212 Arp2/3complex 20 kD subunit, putative TC015671 5.00E−69 213 Elongator complexprotein 2 (ELP2) (STAT3-interacting protein) TC012601 1.00E−68 (StIP1)(SHINC-2) 214 ATP synthase mitochondrial F1 complex assembly factor 2TC013923 3.00E−68 215 Nudt18 protein TC004374 5.00E−68 216NADH:ubiquinone dehydrogenase, putative TC015691 8.00E−68 217 MembrinTC013356 9.00E−68 218 Mitochondrial ribosomal protein L11 TC0095552.00E−67 219 Protein CLEC16A TC005512 2.00E−67 220 15 kDa selenoprotein,putative TC003269 5.00E−67 221 3110057O12Rik protein TC010883 6.00E−67222 Zgc: 123096 TC009382 2.00E−66 223 Methyltransferase-like protein 11ATC013789 2.00E−66 224 Def8 protein, putative TC003420 2.00E−66 225 Zincfinger CCCH domain-containing protein 11A TC007327 6.00E−66 226 Upstreamactivation factor subunit UAF30 TC012018 9.00E−66 227 Phosphatidylserinedecarboxylase TC004926 1.00E−65 228 N-acetyltransferase 9-like proteinTC000126 1.00E−65 229 Alkylated DNA repair protein alkB-like protein 1TC007602 3.00E−65 230 TBC1 domain family TC014792 3.00E−65 231 CG4618TC005451 5.00E−65 232 Exocyst complex component, putative TC0058175.00E−65 233 Mediator of RNA polymerase II transcription subunit 6TC009982 1.00E−64 234 Thioredoxin domain-containing protein 15 TC0053722.00E−64 235 Gualynate kinase-1 (Fragment) TC014210 3.00E−64 236 KTI12protein, putative TC005882 3.00E−64 237 Lymphoid-retiricted membraneprotein, jaw1, putative (Fragment) TC007394 4.00E−64 238Methyltransferase-like protein 9 TC003894 1.00E−63 239 Novel proteinTC010150 2.00E−63 240 Zinc finger FYVE domain-containing protein 19TC009615 2.00E−63 241 Novel protein TC015595 5.00E−63 242 ProteinFAM91A1 TC004359 6.00E−63 243 Protein enabled TC002504 2.00E−62 244Cleavage and polyadenylation specificity factor subunit 6 TC0080143.00E−62 245 Small GTPase, putative TC013254 4.00E−62 246 MultiproteinBridging Factor 1 TC000104 9.00E−62 247 Myb-like protein; Pfam: PF13921TC008316 2.00E−61 248 Protein midA homolog, mitochondrial TC0035653.00E−61 249 Mitochondrial carnitine/acylcarnitine carrier proteinTC012546 5.00E−61 250 COMM domain-containing protein 2 TC014257 7.00E−61251 Ribosomal protein L35A TC002098 7.00E−61 252 Coiled-coildomain-containing protein 93 TC002495 1.00E−60 253 Coiled-coildomain-containing protein MTMR15 TC010140 2.00E−60 254 Methylmalonicaciduria and homocystinuria type D protein, TC000972 2.00E−60mitochondrial 255 Rhomboid protein 1, mitochondrial TC013516 3.00E−60256 Homocysteine-responsive endoplasmic reticulum-resident TC0101607.00E−60 ubiquitin-like domain member 2 protein 257 WH2 protein, Pfam:PF02205 TC012341 8.00E−60 258 WD repeat-containing protein 4 (fragment)TC000064 1.00E−59 259 Vacuolar protein sorting-associated protein16-like protein TC001384 2.00E−59 260 Arp2/3 complex 16 kD subunit,putative TC013790 9.00E−59 261 Novel protein TC008531 1.00E−58 262Mapmodulin, putative TC030635 2.00E−58 263 Ensconsin, isoform E TC0108732.00E−58 264 Casein kinase II subunit beta TC000224 2.00E−58 265Prefoldin subunit 5 TC011234 2.00E−58 266 Deoxynucleotidyltransferaseterminal-interacting protein 2 TC000065 4.00E−58 267 Golgin subfamily Amember 5 TC004294 7.00E−58 268 Lethal neo18 TC004388 4.00E−57 269Pyridoxal kinase TC003259 4.00E−57 270 Putative ARP-like TC0157857.00E−57 271 Mitochondrial ribosomal protein L48 TC007588 2.00E−56 272Splicing factor SPF30 TC005331 3.00E−56 273 Transmembrane protein 208TC003864 4.00E−56 274 Novel protein TC010006 5.00E−56 275 NIF3-likeprotein 1 TC011681 7.00E−56 276 Neuroendocrine protein 7b2 TC0084572.00E−55 277 Class I helical cytokine receptor member 2 TC0002092.00E−55 278 CG8675 TC002245 2.00E−55 279 Novel protein TC0072223.00E−55 280 Dolichyldiphosphatase, putative TC013393 3.00E−55 281 Lowdensity lipoprotein receptor adapter protein 1 TC006386 4.00E−55 282Formin-binding protein 4 TC005008 5.00E−55 283 BRCA1-A complex subunitMERIT40 TC004528 9.00E−55 284 Ribosomal protein L31 TC008311 1.00E−54285 Reticulon; Pfam: PF02453 TC011617 2.00E−54 286 Circadianclock-controlled protein TC013657 3.00E−54 287 Ribosomal protein L28TC003255 5.00E−54 288 Transmembrane domains-containing protein TC0034927.00E−54 289 N-acetyltransferase MAK3-like protein TC008129 2.00E−53 290N-acetyltransferase UNQ2771/PRO7155-like protein TC010378 1.00E−52 291Protein rolling stone TC005180 2.00E−52 292 39S ribosomal protein L32,mitochondrial TC001148 2.00E−52 293 Transcription initiation factorTFIID subunit 13 TC001068 3.00E−52 294 Phosphatidylcholine:ceramidecholinephosphotransferase 1 TC006942 4.00E−52 295 WD40 repeat proteinTC015135 5.00E−52 296 Mitochondrial 39S ribosomal protein L27 TC0000795.00E−52 297 TMEM9 domain family member B TC002414 9.00E−52 298 Novelprotein TC008970 1.00E−51 299 Similar to poly(A)-specific ribonuclease,PARN TC005425 1.00E−51 300 Coiled-coil-helix-coiled-coil-helixdomain-containing protein, TC002433 2.00E−51 putative 301 Mitochondrialribosomal protein, S23, putative TC005391 2.00E−51 302 RCC1domain-containing protein 1 TC012016 3.00E−51 303 Equilibrativenucleoside transporter 1 TC008473 3.00E−51 304 Anamorsin homologTC004939 4.00E−51 305 Transcription elongation factor B polypeptide 2TC004834 4.00E−51 306 Biogenesis of lysosome-related organelles complex1 subunit 1 TC012623 4.00E−51 307 NADH dehydrogenase (Ubiquinone) 1 betasubcomplex, 7 TC001945 5.00E−51 308Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunitTC011996 3.00E−50 delta isoform 309 Alpha- and gamma-adaptin-bindingprotein p34 TC007613 4.00E−50 310 Mediator of RNA polymerase IItranscription subunit 28 TC001173 5.00E−50 311 Novel protein TC0023566.00E−50 312 Ca2+/calmodulin-dependent protein kinase TC010591 8.00E−50313 Mitogen-activated protein kinase kinase 1-interacting protein 1TC002357 1.00E−49 314 Vacuolar protein sorting-associated protein 37BTC014972 1.00E−49 315 Tetratricopeptide repeat; Pfam: PF13414 TC0047204.00E−49 316 Putative sodium-coupled neutral amino acid transporter 10TC003653 4.00E−49 317 DDRGK domain-containing protein 1 TC0011716.00E−49 318 Cactin TC008782 1.00E−48 319 Novel protein (Zgc: 91844)TC030671 2.00E−48 320 HIT zinc finger family protein TC014859 2.00E−48321 Mediator of RNA polymerase II transcription subunit 7 TC0075752.00E−48 322 Mitochondrial import inner membrane translocase subunitTIM14 TC010456 2.00E−48 323 Transmembrane protein, putative TC0139195.00E−48 324 Mitochondrial ribosomal protein, L46, putative TC0011441.00E−47 325 Prefoldin subunit 1 TC010530 1.00E−47 326 F-box onlyprotein, putative TC003789 1.00E−47 327 Paraflagellar rod proteinTC010451 2.00E−47 328 Coiled-coil domain-containing protein 95 TC0092493.00E−47 329 Fez1 TC004530 4.00E−47 330 NADH ubiquinone oxidoreductasesubunit, putative TC014412 8.00E−47 331 Protein C10 TC005394 1.00E−46332 Transmembrane protein 32 TC014495 3.00E−46 333 Cell division cycleprotein 123 homolog TC004132 8.00E−46 334 Novel protein TC0004182.00E−45 335 Coiled-coil domain-containing protein 124 TC004658 2.00E−45336 Ubinuclein TC008303 6.00E−45 337 WD40 domain containing protein;Pfam: PF00400 TC005673 7.00E−45 338 Tat binding protein 1(TBP-1); Pfam:PF00539 TC012383 9.00E−45 339 GPI-anchored wall transfer protein 1TC014480 2.00E−44 340 HCaRG protein; Pfam: PF07258 TC012212 9.00E−44 341Mannose-6-phosphate receptor domain-containing protein TC005595 2.00E−43342 Novel protein TC012803 2.00E−43 343 Ribonuclease H2 subunit CTC002570 2.00E−43 344 Pre-mRNA splicing factor SF3B 10 kDa subunit,putative TC016369 2.00E−43 345 Motile sperm domain-containing protein 1TC002877 3.00E−43 346 UPF0586 protein C1778.07 TC009347 4.00E−43 347Mitochondrial NADH:ubiquinone oxidoreductase B14.7 subunit, TC0090257.00E−43 putative 348 Mitochondrial ribosomal protein, L9, putativeTC010194 7.00E−43 349 MKI67 FHA domain-interacting nucleolarphosphoprotein-like TC004828 8.00E−43 350 Mitochondrial ribosomalprotein L1 TC011372 1.00E−42 351 Putative pterin-4-alpha-carbinolaminedehydratase TC010121 2.00E−42 352 Ecsit TC015956 3.00E−42 353 Probable39S ribosomal protein L49, mitochondrial (fragment) TC007075 8.00E−42354 Brinker TC000748 1.00E−41 355 L-aminoadipate-semialdehydedehydrogenase- TC011251 2.00E−41 phosphopantetheinyl transferase 356Insulin-degrading enzyme TC001879 7.00E−41 357 Ubiquitin-fold modifier 1TC007454 8.00E−41 358 Autotransporter adhesin, putative TC0067451.00E−40 359 TGF-beta activated kinase 1 TC005572 3.00E−40 360Cyclin-dependent kinase 2-interacting protein TC009488 4.00E−40 361Cytochrome c oxidase assembly protein cox11 TC003306 2.00E−39 362CKLF-like MARVEL transmembrane domain-containing protein 4 TC0147374.00E−39 363 Small androgen receptor-interacting protein TC0128174.00E−39 364 Stathmin TC013090 4.00E−38 365 Prolactin regulatoryelement-binding protein TC014725 6.00E−38 366 Serine/threonine-proteinphosphatase 4 regulatory subunit 2 TC008382 7.00E−38 367 Zgc: 152651protein TC000873 1.00E−37 368 Fau TC015895 2.00E−37 369 Mitochondrialimport inner membrane translocase subunit Tim10, TC003366 3.00E−37putative 370 NADH dehydrogenase 1 alpha subcomplex subunit 5 TC0306943.00E−37 371 Mitochondrial ribosomal protein, S18A, putative TC0305604.00E−37 372 Nuclear pore complex protein Nup107 TC011645 5.00E−37 373Protein phosphatase 1 regulatory subunit 14C, putative TC012424 5.00E−37374 FAM98A TC011549 5.00E−37 375 RNA-binding protein with serine-richdomain 1 TC005720 8.00E−37 376 Coiled-coil domain-containing protein 58TC000619 8.00E−37 377 28S ribosomal protein S16 TC009884 9.00E−37 378Glyoxylate/hydroxypyruvate reductase A TC014276 3.00E−36 379Transmembrane protein 50A TC009723 3.00E−36 380 NADH dehydrogenase[ubiquinone] 1 subunit C2 TC007636 3.00E−36 381 Mediator complexTC012102 4.00E−36 382 DNL-type zinc finger protein TC030565 4.00E−36 383Ubiquinol-cytochrome c reductase, complex III subunit VII TC0077665.00E−36 384 F13E9.13, mitochondrial TC004031 8.00E−36 385 Protein YIPF6TC008171 2.00E−35 386 BAG domain-containing protein Samui TC0065532.00E−34 387 Amsh TC011383 3.00E−34 388 Transcription elongation factor1-like protein TC030554 5.00E−34 389 Tumor protein p53-inducible nuclearprotein 1 TC004030 6.00E−34 390 Novel protein TC006224 7.00E−33 391Guanine nucleotide-releasing factor 2 TC004461 1.00E−32 392 Novelprotein TC009815 3.00E−32 393 Mitochondrial NADH-ubiquinoneoxidoreductase 9 kDa subunit- TC007332 5.00E−32 like protein 394Sirtuin-5 TC005187 4.00E−31 395 TP53RK-binding protein TC006547 2.00E−30396 Transferrin (Fragment) TC030767 5.00E−30 397 Novel protein TC0141671.00E−29 398 Regulatory factor X domain-containing protein 2 TC0089591.00E−29 399 Novel protein TC012215 6.00E−29 400 Polyadenylate-bindingprotein-interacting protein, putative TC004150 1.00E−28 401 PallidinTC008878 2.00E−27 402 Signal recognition particle 14 kDa proteinTC030566 2.00E−27 403 Proteasome assembly chaperone 2 TC002896 2.00E−27404 Zinc finger protein 509 TC030550 3.00E−27 405 Polyglutamine-bindingprotein, putative TC014489 2.00E−26 406 HCaRG protein; Pfam: PF07258TC004291 2.00E−26 407 Protein lunapark-B TC009502 4.00E−26 408Polyadenylate-binding protein-interacting protein 1 TC003208 5.00E−26409 Peptidase family S49 N-terminal; Pfam: PF08496 TC002531 6.00E−26 410alba-like protein; Pfam: PF01918 TC006278 1.00E−25 411Pre-rRNA-processing protein TSR2; Pfam: PF10273 TC003011 4.00E−25 412Ribosome-associated membrane protein TC003121 7.00E−25 413 Novel proteinTC007255 3.00E−24 414 Intraflagellar transport protein 122-like proteinTC009862 4.00E−24 415 Chromatin accessibility complex protein 1 TC0058101.00E−22 416 Cag pathogenicity island protein Cag12; Pfam: PF13117TC003712 4.00E−22 417 Novel protein TC013025 1.00E−21 418 MitochondrialNADH:ubiquinone oxidoreductase ESSS subunit, TC030690 2.00E−21 putative419 Novel protein TC002622 3.00E−21 420 Pogo transposable element withZNF domain TC014398 4.00E−21 421 Exopolysaccharide synthesis, ExoD;Pfam: PF06055 TC001378 7.00E−21 422 Transcription elongation factor Bpolypeptide, putative TC001477 1.00E−20 423 Coiled-coildomain-containing protein 137 TC006678 1.00E−20 424Glucocorticoid-induced transcript 1 protein TC001670 2.00E−20 425 24 kDasalivary protein TC007968 5.00E−20 426 CD151 antigen, putative TC0082427.00E−20 427 Novel protein TC001918 1.00E−19 428 WW domain bindingprotein 4 TC011685 2.00E−19 429 Angiogenic factor with G patch and FHAdomains 1 TC009165 2.00E−19 430 Novel protein TC003588 3.00E−19 431Chloride ion current inducer protein, putative TC003587 4.00E−19 432Tetratricopeptide repeat protein 7B TC001250 1.00E−18 433 ProteinHSPC020 homolog TC004459 1.00E−18 434 NADH dehydrogenase TC0040011.00E−18 435 Putative mitochondrial precursor protein; Pfam: PF10161TC012057 6.00E−18 436 Protein dispatched TC010878 3.00E−16 437 Zincfinger CCHC domain-containing protein 10 TC010699 3.00E−16 438 Novelprotein TC013714 5.00E−16 439 Protein HBXIP-like protein TC0068178.00E−16 440 Novel protein TC002312 8.00E−15 441 DSS1/SEM1 family; Pfam:PF05160 TC003531 9.00E−15 442 Novel protein TC003092 1.00E−14 443 Novelprotein TC010373 8.00E−14 444 Mitotic phosphoprotein 67 (Fragment)TC008670 8.00E−13 445 Novel protein TC014221 2.00E−12 446 CDNA sequenceTC030548 2.00E−12 447 C2H2-type zinc finger; Pfam: PF13912 TC0071196.00E−12 448 Novel protein TC006599 2.00E−09 449 Novel protein TC0081472.00E−08 450 4F5 protein family; Pfam: PF04419 TC004123 4.00E−06

This subset of Diabrotica virgifera virgifera genes is selected astarget genes that are likely to be effective targets for RNAi-mediatedsilencing methods. These nucleotide sequences (SEQ ID NOs:1-450) areespecially useful in designing recombinant polynucleotides forcontrolling Diabrotica species infestations, and in making transgenicplants expressing such recombinant polynucleotides for resistance toDiabrotica species infestations.

Example 3

The polynucleotides of this invention are generally designed to modulateexpression by inducing regulation or suppression of a Diabrotica speciestarget gene and are designed to have a nucleotide sequence essentiallyidentical or essentially complementary to the nucleotide sequence of aDiabrotica species target gene (e. g., SEQ ID NOs:1-450) or to thesequence of RNA transcribed from a Diabrotica species target gene, whichcan be coding sequence or non-coding sequence. These effectivepolynucleotide molecules that modulate expression are referred to hereinas a “trigger”, or “triggers”. This example describes non-limitingtechniques useful in the design and selection of polynucleotides as“triggers” to modulate expression of a Diabrotica species target gene.

Selection of Polynucleotide Triggers by “Tiling”

Polynucleotides of use in the invention need not be of the full lengthof a target gene, and in many embodiments are of much shorter length incomparison to the target gene. An example of a technique that is usefulfor selecting effective triggers is “tiling”, or evaluation ofpolynucleotides corresponding to adjacent or partially overlappingsegments of a target gene.

Effective polynucleotide “triggers” can be identified by “tiling” genetargets in selected length fragments, e. g., fragments of 200-300nucleotides in length, with partially overlapping regions, e. g., ofabout 25 nucleotides, along the length of the target gene. To suppress asingle gene, trigger sequences are designed to correspond to (have anucleotide identity or complementarity with) regions that are unique tothe target gene; the selected region of the target gene can includecoding sequence or non-coding sequence (e. g., promoter regions, 3′untranslated regions, introns and the like) or a combination of both.

Where it is of interest to design a target effective in suppressingmultiple target genes, the multiple target gene sequences are alignedand polynucleotide triggers designed to correspond to regions with highsequence homology in common among the multiple targets. Conversely,where it is of interest to design a target effective in selectivelysuppressing one among multiple target sequences, the multiple targetgene sequences are aligned and polynucleotide triggers designed tocorrespond to regions with no or low sequence homology in common amongthe multiple targets.

In a non-limiting example, anti-sense single-stranded RNA triggers aredesigned for each of the target genes listed in Table 1 as follows.Multiple anti-sense single-stranded RNA triggers, each of 200-300nucleotides in length and with a sequence corresponding to (i. e., foranti-sense triggers, complementary to) a fragment of a target genehaving a sequence selected from SEQ ID NOs:1-450 are designed so thateach trigger's sequence overlaps about 25 nucleotides of the nextadjacent trigger's sequence, in such a way that the multiple triggers incombination cover the full length of the target gene. (Sense triggersare designed in an analogous fashion, where the trigger sequence isidentical to a fragment of the target gene. Similarly, double-strandedtriggers can be designed by providing pairs of sense and anti-sensetriggers, each pair of triggers overlapping the next adjacent pair oftriggers.)

The polynucleotide triggers are tested by any convenient means forefficacy in silencing the Diabrotica species target gene. An example ofa suitable test is a diet bioassay such as the Western corn rootworm(Diabrotica virgifera virgifera LeConte) larval bioassay described inInternational Patent Application Publication WO2005/110068 A2 and U.S.Patent Application Publication US 2006/0021087 A1, specificallyincorporated by reference. Another test involves the topical applicationof the polynucleotide triggers either directly to Diabrotica individualsor to the surface of a plant to be protected from a Diabrotica speciesinfestation. One desired result of treatment with a polynucleotide ofthis invention is prevention or control of a Diabrotica speciesinfestation, e. g., by inducing in a Diabrotica insect a physiologicalor behavioural change such as, but not limited to, growth stunting,increased mortality, decrease in reproductive capacity, decrease in orcessation of feeding behavior or movement, or decrease in or cessationof metamorphosis stage development. Another desired result of treatmentwith a polynucleotide of this invention is provision of a plant thatexhibits improved resistance to a Diabrotica species infestation, suchas a maize (Zea mays) plant that exhibits improved resistance to aninfestation by Diabrotica virgifera virgifera (Western Corn Rootworm,WCR), Diabrotica undecimpunctata howardii (Southern Corn Rootworm, SCR),Diabrotica barberi (Northern Corn Rootworm, NCR), Diabrotica virgiferazeae (Mexican Corn Rootworm, MCR), Diabrotica balteata (Brazilian CornRootworm, BZR), or Brazilian Corn Rootworm complex (BCR) consisting ofDiabrotica viridula and Diabrotica speciosa.

The tiling procedure can be repeated, if desired. A polynucleotidetrigger found to provide desired activity can itself be subjected to atiling procedure. For example, multiple overlapping anti-sensesingle-stranded RNA triggers are designed, each of 50-60 nucleotides inlength and with a sequence corresponding to (i. e., for anti-sensetriggers, complementary to) the fragment of a target gene having asequence selected from SEQ ID NOs:1-450 for which a singlepolynucleotide trigger of 300 nucleotides was found to be effective.Additional rounds of tiling analysis can be carried out, where triggersas short as 18 or 19 nucleotides are tested.

Effective polynucleotide triggers of any size can be used, alone or incombination, in the various methods of this invention. In someembodiments, a single polynucleotide trigger is used to make acomposition of this invention (e. g., a composition for topicalapplication, or a recombinant DNA construct useful for making atransgenic plant). In other embodiments, a mixture or pool of differentpolynucleotide triggers is used; in such cases the polynucleotidetriggers can be for a single target gene or for multiple target genes.

Thermodynamic Considerations in Selecting Polynucleotide Triggers

Polynucleotide triggers can be designed or their sequence optimisedusing thermodynamic considerations. For example, polynucleotide triggerscan be selected based on the thermodynamics controlling hybridizationbetween one nucleic acid strand (e. g., a polynucleotide trigger or anindividual siRNA) and another (e. g., a target gene transcript)

Methods and algorithms to predict nucleotide sequences that are likelyto be effective at RNAi-mediated silencing of a target gene are known inthe art. Non-limiting examples of such methods and algorithms include“i-score”, described by Ichihara et al. (2007) Nucleic Acids Res.,35(18): 123e; “Oligowalk”, publicly available atrna.urmc.rochester.edu/servers/oligowalk and described by Lu et al.(2008) Nucleic Acids Res., 36:W104-108; and “Reynolds score”, describedby Khovorova et al. (2004) Nature Biotechnol., 22:326-330.

Permitted Mismatches

By “essentially identical” or “essentially complementary” is meant thatthe trigger polynucleotide (or at least one strand of a double-strandedpolynucleotide) has sufficient identity or complementarity to the targetgene or to the RNA transcribed from a target gene (e. g., thetranscript) to suppress expression of a target gene (e. g., to effect areduction in levels or activity of the target gene transcript and/orencoded protein). Polynucleotides of this invention need not have 100percent identity or complementarity to a target gene or to the RNAtranscribed from a target gene to suppress expression of the target gene(e. g., to effect a reduction in levels or activity of the target genetranscript or encoded protein, or to provide control of a Diabroticaspecies). In some embodiments, the polynucleotide or a portion thereofis designed to be essentially identical to, or essentially complementaryto, a sequence of at least 18 or 19 contiguous nucleotides in either thetarget gene or the RNA transcribed from the target gene. In certainembodiments, an “essentially identical” polynucleotide has 100 percentsequence identity or at least about 83, 84, 85, 86, 87, 88, 89, 90, 91,92, 93, 94, 95, 96, 97, 98, or 99 percent sequence identity whencompared to the sequence of 18 or more contiguous nucleotides in eitherthe endogenous target gene or to an RNA transcribed from the targetgene. In certain embodiments, an “essentially complementary”polynucleotide has 100 percent sequence complementarity or at leastabout 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or99 percent sequence complementarity when compared to the sequence of 18or more contiguous nucleotides in either the target gene or RNAtranscribed from the target gene.

Polynucleotides containing mismatches to the target gene or transcriptcan be used in certain embodiments of the compositions and methods ofthis invention. In some embodiments, the polynucleotide includes atleast 18 or at least 19 contiguous nucleotides that are essentiallyidentical or essentially complementary to a segment of equivalent lengthin the target gene or target gene's transcript. In certain embodiments,a polynucleotide of 19 contiguous nucleotides that is essentiallyidentical or essentially complementary to a segment of equivalent lengthin the target gene or target gene's transcript can have 1 or 2mismatches to the target gene or transcript (i. e., 1 or 2 mismatchesbetween the polynucleotide's 19 contiguous nucleotides and the segmentof equivalent length in the target gene or target gene's transcript). Incertain embodiments, a polynucleotide of 20 or more nucleotides thatcontains a contiguous 19 nucleotide span of identity or complementarityto a segment of equivalent length in the target gene or target gene'stranscript can have 1 or 2 mismatches to the target gene or transcript.In certain embodiments, a polynucleotide of 21 continuous nucleotidesthat is essentially identical or essentially complementary to a segmentof equivalent length in the target gene or target gene's transcript canhave 1, 2, or 3 mismatches to the target gene or transcript. In certainembodiments, a polynucleotide of 22 or more nucleotides that contains acontiguous 21 nucleotide span of identity or complementarity to asegment of equivalent length in the target gene or target gene'stranscript can have 1, 2, or 3 mismatches to the target gene ortranscript.

In designing polynucleotides with mismatches to an endogenous targetgene or to an RNA transcribed from the target gene, mismatches ofcertain types and at certain positions that are more likely to betolerated can be used. In certain exemplary embodiments, mismatchesformed between adenine and cytosine or guanosine and uracil residues areused as described by Du et al. (2005) Nucleic Acids Res., 33:1671-1677.In some embodiments, mismatches in 19 base-pair overlap regions arelocated at the low tolerance positions 5, 7, 8 or 11 (from the 5′ end ofa 19-nucleotide target), at medium tolerance positions 3, 4, and 12-17(from the 5′ end of a 19-nucleotide target), and/or at the hightolerance positions at either end of the region of complementarity, i.e., positions 1, 2, 18, and 19 (from the 5′ end of a 19-nucleotidetarget) as described by Du et al. (2005) Nucleic Acids Res.,33:1671-1677. Tolerated mismatches can be empirically determined inroutine assays, e. g., in in vitro dietary assays on Diabrotica specieslarvae.

Embedding Active Triggers in Neutral Sequence

In an embodiment, a bioactive trigger (i. e., a polynucleotide with asequence corresponding to the target gene and which is responsible foran observed suppression of the target gene) is embedded in “neutral”sequence, i. e., inserted into additional nucleotides that have nosequence identity or complementarity to the target gene. Neutralsequence can be desirable, e. g., to increase the overall length of apolynucleotide. For example, it can be desirable for a polynucleotide tobe of a particular size for reasons of stability, cost-effectiveness inmanufacturing, or biological activity.

It has been reported that for Diabrotica virgifera virgifera dsRNAsgreater than or equal to approximately 60 base-pairs (bp) are requiredfor biological activity in artificial diet bioassays; see Bolognesi etal. (2012) PLoS ONE 7(10): e47534. Thus, in one embodiment, a21-base-pair dsRNA trigger corresponding to a target gene in Table 1 andfound to provide control of a Diabrotica infestation is embedded inneutral sequence of an additional 39 base pairs, thus forming apolynucleotide of about 60 base pairs. In another embodiment, a single21-base-pair trigger is found to be efficacious when embedded in largersections of neutral sequence, e. g., where the total polynucleotidelength is from about 60 to about 300 base pairs.

Example 4

This example illustrates a non-limiting assay useful for evaluating theDiabrotica-controlling efficacy of a polynucleotide of this inventionincluding at least 18 contiguous nucleotides that are essentiallyidentical or complementary to a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ IDNOs:1-450, or including at least 18 contiguous nucleotides that areessentially identical or complementary to a segment of equivalent lengthof a DNA of a target gene selected from the group consisting of thegenes identified in Table 1, or compositions including suchpolynucleotides.

Double-stranded RNA (dsRNA) triggers for each of the target genes with asequence selected from SEQ ID NOs:1-450 (i. e., the 450 target genesidentified in Table 1) are designed and selected as described inExamples 2 and 3 and are tested in a bioassay. Each trigger is about 500base pairs in length with a sequence of contiguous nucleotidescorresponding to an open reading frame of a target gene with a sequenceselected from SEQ ID NOs:1-450 (i. e., a target gene selected from the450 target genes identified in Table 1); where the open reading frame isshorter than 500 nucleotides, a shorter trigger is used. At least onetrigger for each of the 450 target genes is tested; for selected targetgenes multiple triggers are tested. The triggers are chemicallysynthesized by in vitro transcription using a T7 RNA polymerase, usingstandard methodology. The RNA transcription products are purified fromthe T7 reaction mixture and are used either directly in the bioassay orare modified prior to the bioassay by digestion with RNAse III (AmbionCorporation, Austin, Tex.) or DICER (Stratagene, La Jolla, Calif.) toproduce twenty-one and twenty-two nucleotide duplexes containing 5′phosphorylated ends and 3′ hydroxyl ends with 2-3 base overhangs. ThedsRNA triggers for suppressing each of the 450 target genes are testedin a diet bioassay using Diabrotica virgifera virgifera larvae, whereinmortality or stunting of the larvae due to contact with or ingestion ofthe polynucleotide triggers is assayed, is carried out as follows.

Diabrotica virgifera virgifera (WCR) eggs are obtained from CropCharacteristics, Inc., Farmington, Minn. The non-diapausing WCR eggs areincubated in soil for about 13 days at 24 degrees Celsius, 60% relativehumidity, in complete darkness. On day 13 the soil containing WCR eggsis placed between #30- and #60-mesh sieves and the eggs are washed outof the soil with water from a hose. The eggs are surface-disinfected bysoaking in a LYSOL® (Reckitt Benckiser LLC, Parsippany, N.J.) solutionfor three minutes, rinsed three times with sterile water, washed onetime with a 10% formalin solution and then rinsed three additional timesin sterile water. The eggs are then dispensed onto sterile coffeefilters and hatched overnight at 27 degrees Celsius, 60% relativehumidity, in complete darkness.

Insect diet is prepared essentially according to Pleau et al. (2002)Entomologia Experimentalis et Applicata, 105:1-11, with somemodifications. 9.4 grams of Serva agar is dispensed into 540 millilitersof purified water and agitated until the agar is thoroughly distributed.The water/agar mixture is heated to boiling to completely dissolve theagar, and poured into a Waring blender. The blender is maintained at lowspeed while 62.7 grams of Bio-Serv mix (F9757), 3.75 grams lyophilizedmaize root, 1.25 milliliters of green food coloring, and 0.6 millilitersof formalin are added to the hot agar mixture. The mixture is thenadjusted to pH 9.0 with the addition of a 10% potassium hydroxidesolution. The approximately 600 milliliter volume of liquid diet iscontinually mixed at high speed and maintained at from about 48 to about60 degrees Celsius using a sterilized Nalgene-coated magnetic stir baron a magnetic stirring hot plate while being dispensed in aliquots of200 microliters into each well of FALCON 96-well round bottom microtiterplates. The diet in the plates is allowed to solidify and air dry in asterile biohood for about ten minutes.

Thirty (30) microliter volumes of test samples, containing eithercontrol reagents or the polynucleotide (dsRNA triggers) to be tested invarying quantities, are overlayed onto the surface of the solidifiedinsect diet in each well. The plates are allowed to stand in a sterilebiohood for up to one half hour after application of test samples toallow the reagents to diffuse into the diet and to allow the surface ofthe diet to dry. One WCR neonate larva is deposited in each well with afine paintbrush. Plates are then sealed with Mylar and ventilated usingan insect pin. From 12 to 72 larvae are tested per dose, depending onthe design of the assay. The bioassay plates are incubated at 27 degreesCelsius, 60% relative humidity, in complete darkness for 12-14 days.Mortality or stunting of the larvae is observed at the last (12-14) daytime point: the number of surviving larvae per dose is recorded andlarval mass is determined by weighing each surviving larva with ananalytical balance. Data are analyzed using JMP©4 statistical software(SAS Institute, 1995) and a full factorial ANOVA is conducted with aDunnett's test to look for treatment effects compared to the untreatedcontrol (P<0.05). A Tukey-Kramer post hoc test is performed to compareall pairs of the treatments (P<0.05).

It is anticipated that the combination of certain recombinant RNAs ofthis invention (e. g., the dsRNA triggers described herein) with one ormore non-polynucleotide pesticidal agents will result in a synergeticimprovement in prevention or control of Diabrotica species infestations,when compared to the effect obtained with the recombinant RNA alone orthe non-polynucleotide pesticidal agent alone. Routine insect bioassayssuch as the bioassay employing an artificial diet described here areuseful for defining dose-responses for larval mortality or growthinhibition using combinations of the polynucleotides of this inventionand one or more non-polynucleotide pesticidal agents (e. g., a patatin,a plant lectin, a phytoecdysteroid, a Bacillus thuringiensisinsecticidal protein, a Xenorhabdus insecticidal protein, a Photorhabdusinsecticidal protein, a Bacillus laterosporous insecticidal protein, anda Bacillus sphearicus insecticidal protein). One of skill in the art cantest combinations of polynucleotides and non-polynucleotide pesticidalagents in routine bioassays to identify combinations of bioactives thatare synergistic and desirable for use in protecting plants fromDiabrotica species infestations.

Example 5

This example illustrates non-limiting embodiments of the use ofpolynucleotides of this invention in topically applied compositions forpreventing or controlling Diabrotica species infestations.

Compositions containing one or more polynucleotides of this inventionare useful as topical treatments of plants, animals, or environmentswherein prevention or control of a Diabrotica species infestation isdesired. In embodiments, a polynucleotide of this invention (e. g., adsRNA trigger for each of the target genes with a sequence selected fromSEQ ID NOs:1-450, i. e., the 450 target genes identified in Table 1, asdescribed in Examples 3 and 4 above) is included in an effective amountin a composition designed to be provided directly (e. g., by contact oringestion) to a Diabrotica species, or a plant or environment whereinprevention or control of infestation by that Diabrotica species isdesired. Such compositions are formulated and manufactured according tothe art and can be in any convenient form, e. g., a solution or mixtureof solutions, an emulsion, a suspension, a dispersible powder, a solidor liquid bait, a seed coating, or a soil drench. Embodiments of suchcompositions include those where the polynucleotide of this invention isprovided in a living or dead microorganism such as a bacterium or fungalor yeast cell, or provided as a microbial fermentation product, orprovided in a living or dead plant cell, or provided as a syntheticrecombinant polynucleotide. In an embodiment the composition includes anon-pathogenic strain of a microorganism that contains a polynucleotideof this invention; ingestion or intake of the microorganism results instunting or mortality of the Diabrotica species; non-limiting examplesof suitable microorganisms include E. coli, B. thuringiensis,Pseudomonas sp., Photorhabdus sp., Xenorhabdus sp., Serratia entomophilaand related Serratia sp., B. sphaericus, B. cereus, B. laterosporus, B.popilliae, Clostridium bifermentans and other Clostridium species, orother spore-forming gram-positive bacteria. In an embodiment, thecomposition includes a plant virus vector including a polynucleotide ofthis invention; feeding by a Diabrotica species on a plant treated withthe plant virus vector results in stunting or mortality of theDiabrotica species. In an embodiment, the composition includes abaculovirus vector including a polynucleotide of this invention;ingestion or intake of the vector results in stunting or mortality ofthe Diabrotica species. In an embodiment, a polynucleotide of thisinvention is encapsulated in a synthetic matrix such as a polymer orattached to particulates and topically applied to the surface of aplant; feeding by a Diabrotica species on the topically treated plantresults in stunting or mortality of the Diabrotica species. In anembodiment, a polynucleotide of this invention is provided in the formof a plant cell (e. g., a transgenic maize plant cell of this invention)expressing the polynucleotide; ingestion of the plant cell or contentsof the plant cell by a Diabrotica species results in stunting ormortality of the Diabrotica species.

Such compositions can include the appropriate stickers and wettersrequired for efficient foliar coverage as well as UV protectants toprotect polynucleotides such as dsRNAs from UV damage. Such additivesare commonly used in the bioinsecticide industry and are known to thoseskilled in the art. Compositions for soil application can includegranular formulations that serve as bait for Diabrotica species larvae.Such compositions can include a carrier agent, a surfactant, anorganosilicone, a polynucleotide herbicidal molecule, anon-polynucleotide herbicidal molecule, a non-polynucleotide pesticide,a safener, and an insect growth regulator. In embodiments, thecomposition further includes at least one pesticidal agent selected fromthe group consisting of a patatin, a plant lectin, a phytoecdysteroid, aBacillus thuringiensis insecticidal protein, a Xenorhabdus insecticidalprotein, a Photorhabdus insecticidal protein, a Bacillus laterosporousinsecticidal protein, and a Bacillus sphearicus insecticidal protein.

Such compositions are applied in any convenient manner, e. g., byspraying or dusting the Diabrotica species directly, or spraying ordusting a plant or environment wherein prevention or control ofinfestation by that Diabrotica species is desired, or by applying acoating to a surface of a plant, or by applying a coating to a seed inpreparation for the seed's planting, or by applying a soil drench aroundroots of a plant for which prevention or control of infestation by thatDiabrotica species is desired.

An effective amount of a polynucleotide of this invention is an amountsufficient to provide control of the Diabrotica species, or to preventinfestation by the Diabrotica species; determination of effectiveamounts of a polynucleotide of this invention are made using routineassays such as those described in Example 4 above. While there is noupper limit on the concentrations and dosages of a polynucleotide ofthis invention that can be useful in the methods and compositionsprovided herein, lower effective concentrations and dosages willgenerally be sought for efficiency. The concentrations can be adjustedin consideration of the volume of spray or treatment applied to plantleaves or other plant part surfaces, such as flower petals, stems,tubers, fruit, anthers, pollen, leaves, roots, or seeds. In oneembodiment, a useful treatment for herbaceous plants using 25-merpolynucleotides of this invention is about 1 nanomole (nmol) ofpolynucleotides per plant, for example, from about 0.05 to 1 nmolpolynucleotides per plant. Other embodiments for herbaceous plantsinclude useful ranges of about 0.05 to about 100 nmol, or about 0.1 toabout 20 nmol, or about 1 nmol to about 10 nmol of polynucleotides perplant. In certain embodiments, about 40 to about 50 nmol of a ssDNApolynucleotide of this invention is applied. In certain embodiments,about 0.5 nmol to about 2 nmol of a dsRNA of this invention is applied.In certain embodiments, a composition containing about 0.5 to about 2.0mg/mL, or about 0.14 mg/mL of a dsRNA or an ssDNA (21-mer) of thisinvention is applied. In certain embodiments, a composition of about 0.5to about 1.5 mg/mL of a dsRNA polynucleotide of this invention of about50 to about 200 or more nucleotides is applied. In certain embodiments,about 1 nmol to about 5 nmol of a dsRNA of this invention is applied toa plant. In certain embodiments, the polynucleotide composition astopically applied to the plant contains at least one polynucleotide ofthis invention at a concentration of about 0.01 to about 10 milligramsper milliliter, or about 0.05 to about 2 milligrams per milliliter, orabout 0.1 to about 2 milligrams per milliliter Very large plants, trees,or vines can require correspondingly larger amounts of polynucleotides.When using long dsRNA molecules of this invention that can be processedinto multiple oligonucleotides (e. g., multiple triggers encoded by asingle recombinant DNA molecule of this invention), lower concentrationscan be used. Non-limiting examples of effective polynucleotide treatmentregimes include a treatment of between about 0.1 to about 1 nmol ofpolynucleotide molecule per plant, or between about 1 nmol to about 10nmol of polynucleotide molecule per plant, or between about 10 nmol toabout 100 nmol of polynucleotide molecule per plant.

Embodiments of compositions of this invention include a “transferagent”, i. e., an agent that, when combined with a composition includinga polynucleotide of this invention that is topically applied to thesurface of an organism, enables the polynucleotide to enter the cells ofthat organism. Such transfer agents can be incorporated as part of thecomposition including a polynucleotide of this invention, or can beapplied prior to, contemporaneously with, or following application ofthe composition including a polynucleotide of this invention. Inembodiments, a transfer agent is an agent that improves the uptake of apolynucleotide of this invention by a Diabrotica species. Inembodiments, a transfer agent is an agent that conditions the surface ofplant tissue, e. g., seeds, leaves, stems, roots, flowers, or fruits, topermeation by a polynucleotide of this invention into plant cells. Inembodiments, the transfer agent enables a pathway for a polynucleotideof this invention through cuticle wax barriers, stomata, and/or cellwall or membrane barriers into plant cells.

Suitable transfer agents include agents that increase permeability ofthe exterior of the organism or that increase permeability of cells ofthe organism to polynucleotides of this invention. Suitable transferagents include a chemical agent, or a physical agent, or combinationsthereof. Chemical agents for conditioning or transfer include (a)surfactants, (b) an organic solvent or an aqueous solution or aqueousmixtures of organic solvents, (c) oxidizing agents, (d) acids, (e)bases, (f) oils, (g) enzymes, or combinations thereof. In embodiments,application of a composition of this invention and a transfer agentoptionally includes an incubation step, a neutralization step (e. g., toneutralize an acid, base, or oxidizing agent, or to inactivate anenzyme), a rinsing step, or combinations thereof. Suitable transferagents can be in the form of an emulsion, a reverse emulsion, aliposome, or other micellar-like composition, or can cause thepolynucleotide composition to take the form of an emulsion, a reverseemulsion, a liposome, or other micellar-like composition. Embodiments oftransfer agents include counter-ions or other molecules that are knownto associate with nucleic acid molecules, e. g., inorganic ammoniumions, alkyl ammonium ions, lithium ions, polyamines such as spermine,spermidine, or putrescine, and other cations. Embodiments of transferagents include organic solvents such as DMSO, DMF, pyridine,N-pyrrolidine, hexamethylphosphoramide, acetonitrile, dioxane,polypropylene glycol, or other solvents miscible with water or thatdissolve phosphonucleotides in non-aqueous systems (such as is used insynthetic reactions). Embodiments of transfer agents include naturallyderived or synthetic oils with or without surfactants or emulsifiers, e.g., plant-sourced oils, crop oils (such as those listed in the 9^(th)Compendium of Herbicide Adjuvants, publicly available on-line atherbicide.adjuvants.com), paraffinic oils, polyol fatty acid esters, oroils with short-chain molecules modified with amides or polyamines suchas polyethyleneimine or N-pyrrolidine.

Embodiments of transfer agents include organosilicone preparations. Forexample, a suitable transfer agent is an organosilicone preparation thatis commercially available as Silwet® L-77 surfactant having CAS Number27306-78-1 and EPA Number: CAL.REG.NO. 5905-50073-AA, and currentlyavailable from Momentive Performance Materials, Albany, N.Y. Inembodiments where a Silwet L-77 organosilicone preparation is used astransfer agent in the form of a spray treatment (applied prior to,contemporaneously with, or following application of the compositionincluding a polynucleotide of this invention) of plant leaves or otherplant surfaces, freshly made concentrations in the range of about 0.015to about 2 percent by weight (wt percent) (e. g., about 0.01, 0.015,0.02, 0.025, 0.03, 0.035, 0.04, 0.045, 0.05, 0.055, 0.06, 0.065, 0.07,0.075, 0.08, 0.085, 0.09, 0.095, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8,0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2,2.3, 2.5 wt percent) are efficacious in preparing a leaf or other plantsurface for transfer of a polynucleotide of this invention into plantcells from a topical application on the surface. One embodiment includesa composition that comprises a polynucleotide of this invention and atransfer agent including an organosilicone preparation such as SilwetL-77 in the range of about 0.015 to about 2 percent by weight (wtpercent) (e. g., about 0.01, 0.015, 0.02, 0.025, 0.03, 0.035, 0.04,0.045, 0.05, 0.055, 0.06, 0.065, 0.07, 0.075, 0.08, 0.085, 0.09, 0.095,0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4,1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.5 wt percent). Oneembodiment includes a composition that comprises a polynucleotide ofthis invention and a transfer agent including Silwet L-77 in the rangeof about 0.3 to about 1 percent by weight (wt percent) or about 0.5 toabout 1% by weight (wt percent).

Organosilicone compounds useful as transfer agents for use in thisinvention include, but are not limited to, compounds that include: (a) atrisiloxane head group that is covalently linked to, (b) an alkyl linkerincluding, but not limited to, an n-propyl linker, that is covalentlylinked to, (c) a polyglycol chain, that is covalently linked to, (d) aterminal group. Trisiloxane head groups of such organosilicone compoundsinclude, but are not limited to, heptamethyltrisiloxane. Alkyl linkerscan include, but are not limited to, an n-propyl linker Polyglycolchains include, but are not limited to, polyethylene glycol orpolypropylene glycol. Polyglycol chains can comprise a mixture thatprovides an average chain length “n” of about “7.5”. In certainembodiments, the average chain length “n” can vary from about 5 to about14. Terminal groups can include, but are not limited to, alkyl groupssuch as a methyl group. Organosilicone compounds useful as transferagents for use in this invention include, but are not limited to,trisiloxane ethoxylate surfactants or polyalkylene oxide modifiedheptamethyl trisiloxane. An example of a transfer agent for use in thisinvention is Compound I:

Organosilicone compounds useful as transfer agents for use in thisinvention are used, e. g., as freshly made concentrations in the rangeof about 0.015 to about 2 percent by weight (wt percent) (e. g., about0.01, 0.015, 0.02, 0.025, 0.03, 0.035, 0.04, 0.045, 0.05, 0.055, 0.06,0.065, 0.07, 0.075, 0.08, 0.085, 0.09, 0.095, 0.1, 0.2, 0.3, 0.4, 0.5,0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9,2.0, 2.1, 2.2, 2.3, 2.5 wt percent).

Embodiments of transfer agents include one or more salts such asammonium chloride, tetrabutylphosphonium bromide, and ammonium sulfate,provided in or used with a composition including a polynucleotide ofthis invention. In embodiments, ammonium chloride, tetrabutylphosphoniumbromide, and/or ammonium sulfate are used at a concentration of about0.5% to about 5% (w/v), or about 1% to about 3% (w/v), or about 2%(w/v). In certain embodiments, the composition including apolynucleotide of this invention includes an ammonium salt at aconcentration greater or equal to 300 millimolar. In certainembodiments, the composition including a polynucleotide of thisinvention includes an organosilicone transfer agent in a concentrationof about 0.015 to about 2 percent by weight (wt percent) as well asammonium sulfate at concentrations from about 80 to about 1200 mM orabout 150 mM to about 600 mM.

Embodiments of transfer agents include a phosphate salt. Phosphate saltsuseful in a composition including a polynucleotide of this inventioninclude, but are not limited to, calcium, magnesium, potassium, orsodium phosphate salts. In certain embodiments, the compositionincluding a polynucleotide of this invention includes a phosphate saltat a concentration of at least about 5 millimolar, at least about 10millimolar, or at least about 20 millimolar. In certain embodiments, thecomposition including a polynucleotide of this invention includes aphosphate salt in a range of about 1 mM to about 25 mM or in a range ofabout 5 mM to about 25 mM. In certain embodiments, the compositionincluding a polynucleotide of this invention includes sodium phosphateat a concentration of at least about 5 millimolar, at least about 10millimolar, or at least about 20 millimolar. In certain embodiments, thecomposition including a polynucleotide of this invention includes sodiumphosphate at a concentration of about 5 millimolar, about 10 millimolar,or about 20 millimolar. In certain embodiments, the compositionincluding a polynucleotide of this invention includes a sodium phosphatesalt in a range of about 1 mM to about 25 mM or in a range of about 5 mMto about 25 mM. In certain embodiments, the composition including apolynucleotide of this invention includes a sodium phosphate salt in arange of about 10 mM to about 160 mM or in a range of about 20 mM toabout 40 mM. In certain embodiments, the composition including apolynucleotide of this invention includes a sodium phosphate buffer at apH of about 6.8.

Embodiments of transfer agents include surfactants and/or effectivemolecules contained therein. Surfactants and/or effective moleculescontained therein include, but are not limited to, sodium or lithiumsalts of fatty acids (such as tallow or tallowamines or phospholipids)and organosilicone surfactants. In certain embodiments, the compositionincluding a polynucleotide of this invention is formulated withcounter-ions or other molecules that are known to associate with nucleicacid molecules. Non-limiting examples include, tetraalkyl ammonium ions,trialkyl ammonium ions, sulfonium ions, lithium ions, and polyaminessuch as spermine, spermidine, or putrescine. In certain embodiments, thecomposition including a polynucleotide of this invention is formulatedwith a non-polynucleotide herbicide e. g., glyphosate, auxin-likebenzoic acid herbicides including dicamba, chloramben, and TBA,glufosinate, auxin-like herbicides including phenoxy carboxylic acidherbicide, pyridine carboxylic acid herbicide, quinoline carboxylic acidherbicide, pyrimidine carboxylic acid herbicide, and benazolin-ethylherbicide, sulfonylureas, imidazolinones, bromoxynil, delapon,cyclohezanedione, protoporphyrinogen oxidase inhibitors, and4-hydroxyphenyl-pyruvate-dioxygenase inhibiting herbicides. In certainembodiments, the composition including a polynucleotide of thisinvention is formulated with a non-polynucleotide pesticide, e. g., apatatin, a plant lectin, a phytoecdysteroid, a Bacillus thuringiensisinsecticidal protein, a Xenorhabdus insecticidal protein, a Photorhabdusinsecticidal protein, a Bacillus laterosporous insecticidal protein, anda Bacillus sphearicus insecticidal protein.

All of the materials and methods disclosed and claimed herein can bemade and used without undue experimentation as instructed by the abovedisclosure. Although the materials and methods of this invention havebeen described in terms of preferred embodiments and illustrativeexamples, it will be apparent to those of skill in the art thatvariations can be applied to the materials and methods described hereinwithout departing from the concept, spirit and scope of this invention.All such similar substitutes and modifications apparent to those skilledin the art are deemed to be within the spirit, scope and concept of thisinvention as defined by the appended claims.

1.-46. (canceled)
 47. A method of causing mortality or stunting inDiabrotica species larvae comprising providing in the diet of Diabroticaspecies larvae at least one recombinant RNA comprising at least onesilencing element essentially identical or essentially complementary toa target gene of said Diabrotica species larvae, wherein said targetgene sequence is selected from the group consisting of SEQ ID NOs:1-450or the complement thereof, and wherein ingestion of said recombinant RNAby said Diabrotica species larvae results in mortality or stunting insaid Diabrotica species larvae.
 48. The method of claim 47, wherein saidDiabrotica species is at least one selected from the group consisting ofDiabrotica balteata, Diabrotica barberi, Diabrotica beniensis,Diabrotica cristata, Diabrotica curvipustulata, Diabrotica dissimilis,Diabrotica elegantula, Diabrotica emorsitans, Diabrotica graminea,Diabrotica hispanolae, Diabrotica lemniscata, Diabrotica linsleyi,Diabrotica longicornis, Diabrotica milleri, Diabrotica nummularis,Diabrotica occlusa, Diabrotica porracea, Diabrotica scutellata,Diabrotica speciosa, Diabrotica tibialis, Diabrotica trifasciata,Diabrotica undecimpunctata, Diabrotica virgifera, and Diabroticaviridula.
 49. The method of claim 47, wherein said Diabrotica species isat least one selected from the group consisting of Diabrotica virgiferavirgifera (Western Corn Rootworm, WCR), Diabrotica undecimpunctatahowardii (Southern Corn Rootworm, SCR), Diabrotica barberi (NorthernCorn Rootworm, NCR), Diabrotica virgifera zeae (Mexican Corn Rootworm,MCR), Diabrotica balteata (Brazilian Corn Rootworm, BZR), or BrazilianCorn Rootworm complex (BCR) consisting of Diabrotica viridula andDiabrotica speciosa.
 50. The method of claim 47, wherein said silencingelement comprises at least 18 contiguous nucleotides with a sequence ofabout 95% to about 100% identity with a segment of equivalent length ofsaid target gene. 51.-97. (canceled)
 98. A method of providing a planthaving improved resistance to a Diabrotica species infestationcomprising expressing in said plant at least one polynucleotidecomprising at least 18 contiguous nucleotides that are essentiallyidentical or complementary to a segment of equivalent length of a DNAhaving a sequence selected from the group consisting of SEQ IDNOs:1-450.
 99. (canceled)
 100. The method of claim 98, wherein saidplant is selected from the group consisting of maize, cucumber, squash,soybeans, and dry beans. 101.-102. (canceled)
 103. The method of claim98, wherein said Diabrotica species is at least one selected from thegroup consisting of Diabrotica balteata, Diabrotica barberi, Diabroticabeniensis, Diabrotica cristata, Diabrotica curvipustulata, Diabroticadissimilis, Diabrotica elegantula, Diabrotica emorsitans, Diabroticagraminea, Diabrotica hispanolae, Diabrotica lemniscata, Diabroticalinsleyi, Diabrotica longicornis, Diabrotica milleri, Diabroticanummularis, Diabrotica occlusa, Diabrotica porracea, Diabroticascutellata, Diabrotica speciosa, Diabrotica tibialis, Diabroticatrifasciata, Diabrotica undecimpunctata, Diabrotica virgifera, andDiabrotica viridula.
 104. The method of claim 98, wherein saidDiabrotica species is at least one selected from the group consisting ofDiabrotica virgifera virgifera (Western Corn Rootworm, WCR), Diabroticaundecimpunctata howardii (Southern Corn Rootworm, SCR), Diabroticabarberi (Northern Corn Rootworm, NCR), Diabrotica virgifera zeae(Mexican Corn Rootworm, MCR), Diabrotica balteata (Brazilian CornRootworm, BZR), or Brazilian Corn Rootworm complex (BCR) consisting ofDiabrotica viridula and Diabrotica speciosa.
 105. The method of claim98, wherein said expressing is by means of transgenic expression ortransient expression.
 106. The method of claim 98, further comprisingexpression in said plant of at least one pesticidal agent selected fromthe group consisting of a patatin, a plant lectin, a phytoecdysteroid, aBacillus thuringiensis insecticidal protein, a Xenorhabdus insecticidalprotein, a Photorhabdus insecticidal protein, a Bacillus laterosporousinsecticidal protein, and a Bacillus sphearicus insecticidal protein.107. The method of claim 98, wherein said identity is 100% identity.108. The plant having improved resistance to a Diabrotica speciesinfestation, provided by the method of claim
 98. 109. Seed of the plantof claim
 98. 110. A recombinant DNA construct comprising a heterologouspromoter operably linked to DNA comprising at least one segment of 18 ormore contiguous nucleotides with a sequence of about 95% to about 100%identity with a segment of equivalent length of a DNA having a sequenceselected from the group consisting of SEQ ID NOs:1-450 or the DNAcomplement thereof.
 111. The recombinant DNA construct of claim 110,wherein said heterologous promoter is selected from the group consistingof a promoter functional in a plant, a promoter functional in aprokaryote, a promoter functional in a fungal cell, and a baculoviruspromoter.
 112. A recombinant vector comprising the recombinant DNAconstruct of claim
 110. 113. The recombinant vector of claim 112,wherein said recombinant vector is a recombinant plant virus vector or arecombinant baculovirus vector.
 114. (canceled)
 115. A plant chromosomeor plastid comprising the recombinant DNA construct of claim
 110. 116. Atransgenic plant cell having in its genome the recombinant DNA constructof claim
 110. 117. A transgenic plant comprising the transgenic plantcell of claim
 116. 118.-195. (canceled)